washington. From: Gianluca Interlandi (gianluca_at_u. What can be the possible cause for this or does it happens naturallyOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. Bioengineering. I am > using the option "wrapAll on". Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Electrical. washington. The difference is usually after the > 4th decimal after the period. On 6 May 2009, at 11:04, Gianluca Interlandi wrote: > Thanks Anton for your answer. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. C; the more troublesome part is the lack of long-range electrostatic treatments. The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor. I'm testing specifically this protein for its beaviour. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. > > NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. The simulations were not performed at constant velocity > but at constant force. washington. I needed to install the 'patch' program. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. g. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. From: Axel Kohlmeyer (akohlmey_at_gmail. edu> wrote: > Hi! > > Are there any benchmarks available which compare the performance of NAMD on > Lincoln (CUDA heterogenous cluster) with its performance on a traditional > CPU only cluster like Abe? >Re: editing the code of the non bonded pair potentials. Biochemistry. how to output more significant figures in a file for energies and forces? Next message: Gianluca Interlandi: "Re: accuracy of measurement"Locking up the spike protein to prevent infection. edu Subject: Re: namd-l: DCD Load your psf+dcd into VMD. Choose File -> Save Coordinates. From: Gianluca Interlandi (gianluca_at_u. Try copying it again from where the simulation was run. washington. One of the. edu> wrote:Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. Semantic Scholar's Logo. To: Gianluca Interlandi <gianluca_at_u. Next in thread: Gianluca Interlandi: "Re: namd-l: DCD for windows" Messages sorted by: [ attachment ] Hi, We don't have a build of catdcd for windows currently, but it should be possible to make one. > > > > Forget about creating a pdb file. Biochemistry. PMID: 37700555; DOI: 10. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino:. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. Sarah Keller Professor. edu) Date: Thu Apr 07 2011 - 16:55:51 CDT Next message: THANH NGUYEN: "SMD simulation: stop applying force during simulation?" Previous message: johan strumpfer: "Re: Abe versus Lincoln" In reply to: johan strumpfer: "Re:. uiuc. Display options Format Abstract The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved. 122076 s/step, which is 16% slower than using > the 6Re: Question about equilibration. From: Gianluca Interlandi (gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). From: Gianluca Interlandi (gianluca_at_u. Justin Kollman Professor. edu) Date: Thu Apr 07 2011 - 16:55:51 CDT Next message: THANH NGUYEN: "SMD simulation: stop applying force during simulation?" Previous message: johan strumpfer: "Re: Abe versus Lincoln" In reply to: johan strumpfer: "Re:. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. 6 ns/day for a 100k atom system with roughly those same parameters (and. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. 478 KJ/mol = 0. edu) Date: Tue Jul 15 2014 - 22:32:35 CDT Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne,. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). Hope the video helps, but now I'm embarrassed. washington. Next in thread: Gianluca Interlandi: "Re: NAMD 2. 7 ns/day, which seems decent given the system size. Biochemistry. washington. Chemistry. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. washington. Academic ProgramsFrom: Gianluca Interlandi (gianluca_at_u. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. 7 out the door on Friday. This school has it's > own biophysics division. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. > > Forget about creating a pdb file. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. washington. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. I empolyed PBC condition with wraping water and wraping all options on. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. 5923 Kcal/mol also we have 6. I would be > happy if somebody could point me out to some scripts which help me performOn Thu, 5 Apr 2012, Gianluca Interlandi wrote: > What is the advantage of the multicore version of charm++ versus net-linux? > Is multicore faster if I'm running for example on a 32-core magny-Cours AMDFrom: Gianluca Interlandi (gianluca_at_u. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. edu> wrote: >> Hi! >> >> Are there any benchmarks available which compare the performance of NAMD on >> Lincoln (CUDA heterogenous cluster) with its performance on a traditionalVMD-L Mailing List. > > Gianluca > > On Wed, 23 Sep 2015, John Stone. You should simulate it in explicit water (or try one of the implicitCompiling NAMD 2. {Gianluca Interlandi and Svava K Wetzel and Giovanni Settanni and Andreas Pl{"u}ckthun and Amedeo Caflisch}, journal={Journal of molecular biology}, year={2008},. The more tasks you have the > more frequently the CPUs need to update each other. Member since 2014. > > Any ideas how it affects the stability of a simulated protein? If On Thu, Jul 12, 2012 at 4:58 PM, Gianluca Interlandi < gianluca_at_u. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]: Gianluca Interlandi (gianluca_at_u. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. washington. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. There have been over 180 downloads and no complaints so far. Hemostasis in vertebrates involves both a cellular and a protein component. washington. But not now. In reply to: Gianluca Interlandi: "Compiling NAMD 2. Bioengineering. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. edu]Reply All Saturday,. edu>: > Dear NAMD users, > > Is it possible to perform Poisson Boltzmann calculation with NAMD? > > I have simulated the wildtype and a single-point mutant of a protein. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. washington. washington. Next in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. I was recording the energies once every 100 steps. What this rental offers. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). Thomas, 2 , * and Evgeni V. Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Re: Help building a desktop for namd. edu> > wrote: > are other people also using those GPUs? > > Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] This archive was generated by Research Assistant Professor gianluca@u. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. Thanks for the reply. In reply to: Gianluca Interlandi: "Vibrational mode analysis" Next in thread: Richard Law: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] CHARMM does normal mode. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. > > I am trying to open VMD remotely. Eric Klavins Professor. washington. washington. washington. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. washington. edu) Date: Thu Apr 05 2012 - 15:44:43 CDT Next message: Gianluca Interlandi: "Re: DCD" Previous message: Jérôme Hénin: "Re: changing harmonic restraints (colvars)" Next in thread: Gianluca Interlandi: "Re: DCD" Reply: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ]. edu] Sent: Monday, June 20, 2016 12:46 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small> 2011/6/29 Gianluca Interlandi <gianluca_at_u. monu_at_gmail. 0 and 2. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"Previous message: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" In reply to: Aron Broom: "Re: Am I doing the Right Thing?" Next in thread: Aron Broom: "Re: Am I doing the Right Thing?" Reply: Aron Broom: "Re: Am I doing the Right Thing?" Messages sorted by: [ attachment ] Hi Aron, I understand now what you are. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. Friend and Aachal Jalan and Shivani Gupta and Gianluca Interlandi and Yan Liu* and Veronika Tchesnokova. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. It's > slightly faster but still not that much faster than running on 16 CPU cores. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. uiuc. Reply: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] Dear NAMD users, A portion of my protein is outside of the simulation box. washington. edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"From: Gianluca Interlandi (gianluca_at_u. Interlandi Mortgage Consultants, LLC Dec 2008 - Present 14 years 3 months. washington. I would be > happy if somebody could point me out to some scripts which help me perform Hemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". Gianluca Interlandi Research Assistant Professor. edu) Date: Mon Oct 11 2010 - 16:56:03 CDT Next message: Basak Isin: "Re: Regarding answering questions in a forum. washington. She joined Schiller DuCanto & Fleck LLP in 1999 as a law clerk and became partner with the firm in 2009. University of Washington Department of Bioengineering. washington. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. washington. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. Eric Klavins Professor. The only significant change since 2. double. These are the lastIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. (Oct-Nov 1997) Spanish: Fluent written and spoken German: Basic Knowledge WORK EXPERIENCE 2019 October: Founder Host. washington. edu> > wrote:Re: Help building a desktop for namd. I doubt that there is a way to have NAMD output theGianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>@article{Kisiela2015EffectOM, title={Effect of mAb926 and mAb475 on biofilm formed by E. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. washington. washington. C; the more troublesome part is the lack of long-range electrostatic treatments. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. Michel Espinoza-Fonseca: "Re: Vibrational. 0 and 2. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. edu> > wrote:Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. uiuc. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino: "Re: NAMD 2. washington. uiuc. Cancellation policy. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. Gianluca, Yes, I think that a higher damping constant will indeed slow down conformational sampling. Deadline is this Friday (or in three > months). edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. PMID: 37700555; DOI: 10. washington. 1 the measure command of VMD can also > calculate the energy: > > energy energy_term atom_list [parameters] [options]: Returns the > specified energy term for a given set of atoms. From: Gianluca Interlandi (gianluca_at_u. Join Facebook to connect with Gianluca Interlandi and others you may know. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. The simulations were not performed at constant velocity > but at constant force. What are you trying to accomplish?Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a jsLe mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. This is unrelated to KDE3. com) Date: Fri Aug 30 2013 - 18:19:04 CDT Next message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" Previous message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" In reply to:. E-mail: [email protected],. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. Facilities. 7 released. Previous message: Gianluca Interlandi: "NAMD 2. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected] on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallConvert solvated CHARMM PDB + PSF to Amber. Michel Espinoza-Fonseca: "Re: Vibrational. Biochemistry. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. Living Room. 26588 Item in Clipboard Cite. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. washington. From: Gianluca Interlandi (gianluca_at_u. washington. at 298. GianlucaHosted by Gianluca Interlandi. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. washington. edu]Reply All Saturday,. Proteins 78, 2506–2522 [PMC free article] [Google Scholar]Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. txt". washington. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi (gianluca_at_u. A 1 TB > Samsung Evo 850 Pro costs 470$, a 1 TB Intel costs ~ 600$ and a PCIe Intel > 1 TB is over 2000$. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. Hope the video helps, but now I'm embarrassed. 1002/prot. Thanks for the reply. 7 ns/day, which seems decent given the system size. washington. edu > <mailto:gianluca_at_u. Both > simulations were started from X-ray structures. gov) Date: Fri Jun 18 2004 - 14:48:36 CDT Next message: Gianluca Interlandi: "Re: recentering protein in the waterbox" Previous message: Jerry Ebalunode: "recentering protein in the waterbox" Messages sorted by: [ attachment ] Hello, I'm running namd and am getting the following errors as itsIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping. uiuc. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. 97 pN*nm = 1 Kcal/molOn Wed, Nov 26, 2014 at 04:06:03PM -0800, Gianluca Interlandi wrote: > Dear vmd list, > > I noticed that I get slightly different results when I measure the > distance between two atoms using "measure bond" vs by measuring the length > of the vector between the two atoms. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. washington. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. From: John Stone (johns_at_ks. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" INVENTING THE FUTURE OF MEDICINE. Re: replica exchange and GPU acceleration. I did what you and Gianluca suggested but still have two caveats. edu> wrote: > Hi, > > Can the current version of NAMD be used together with the new CHARMM36 force > field? The parameter files are "top_all36_prot. washington. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. edu) Date: Mon Apr 11 2011 - 14:41:28 CDT Next message: Axel Kohlmeyer: "Re: Help building a desktop for namd" Previous message: Buddhadev Maiti: "(no subject)" In reply to: Axel Kohlmeyer: "Re: Help building a desktop for namd" Next in. washington. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread: Maxime Boissonneault: "Re: namd ibverbs" The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. 7 On Wed, Sep 18, 2013 at 11:43:49AM -0700, Gianluca Interlandi wrote: > Dear VMD list, > > I think that this question was asked previously. From: Gianluca Interlandi (gianluca_at_u. washington. washington. edu> > wrote: > are other people also using those GPUs? > >In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. From: Gianluca Interlandi (gianluca_at_u. I have a new computer that came with Windows 10, which uses UEFI with a disk that has a GPT label. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. Location info. At the point of breaking the temperature raises of a few> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. I wonder whether anybody > has had the same problem and found a solution. washington. From: Gianluca Interlandi (gianluca_at_u. I made those videos seven years ago. by G. Michel Espinoza-Fonseca: "Re: Vibrational. However, using monoclonal antibodies specific for the mannose-binding Escherichia coli. On Thu, Apr 09, 2015 at 03:39:49PM -0700, Gianluca Interlandi wrote: > Dear list, > > Starting with version 1. From: Gianluca Interlandi (gianluca_at_u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. 26055 Abstract The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. From: Gianluca Interlandi (gianluca_at_u. com) Date: Wed Aug 27 2014 - 22:13:06 CDT Next message: Gianluca Interlandi: "Re:" Previous message: Douglas Houston: "Re: AW: Using nodelist file causes namd to hang" Next in thread: Gianluca Interlandi: "Re:" Reply: Gianluca Interlandi: "Re:" Messages sorted by: [. I thought I will see in my output file the energies stored at times 0 fs, 500 fs,. Search for: Main Menu Author Summary A common approach in the development of selective inhibitors for ligand-receptor interactions is targeting the receptor binding site with the expectation that inhibitors will sterically interfere with ligand binding and thus block receptor function via a competitive (orthosteric) mechanism. From: Gianluca Interlandi (gianluca_at_u. I got 0. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. In this way, you could get a feeling what NAMD can do before you > invest money. > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ attachment ] If that's the only force you are applying to the system, then that is your external work. VMD-L Mailing List. washington. My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. 15 K 1 KT = 2. washington. edu> > wrote: > are other people also using those GPUs? > >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. Sokurenko 1 , *. 7b1 on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallRe: Help building a desktop for namd. Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne, Christopher G: "Re: Force field design" Messages sorted by: [ attachment ] If you are familiar with the CHARMM program, a good resource is:. washington. Usually, this > is > written in the dcd file if you specified "DCDUnitCell yes" in your > NAMD > config file. Neil King Assistant Professor. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. washington. edu> wrote: > I'm cc'ing here the NAMD list so that others. uiuc. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. I would be > happy if somebody could point me out to some scripts which help me performRe: checkpoint software for NAMD? From: Gianluca Interlandi (gianluca_at_u. washington. Try copying it again from where the simulation was run. Gianluca From: Gianluca Interlandi (gianluca_at_u. edu) Date: Tue Sep 15 2020 - 20:34:44 CDT Next message: Kodituwakku,Dimuthu Nirmani: "Re: Post processing NAMD trajectory" Previous message: Victor Zhao: "Re: Re: AMBER input and REST2 leads to crash" Next in thread:. 9. washington. From: Axel Kohlmeyer (akohlmey_at_gmail. From: Stern, Julie (jvstern_at_bnl. washington. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass"In reply to: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ attachment ] If that's the only force you are applying to the system, then that is your external work. MyGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. 100% refund of amount payable if you cancel at least 14 days before check-in. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. washington. washington. washington. 7 ns/day, which seems decent given the system size. 50% refund of amount payable if you cancel at least 7 days before check-in. edu> wrote: In reply to: Gianluca Interlandi: "Compiling NAMD 2. From: Gianluca Interlandi (gianluca_at_u. > > gianluca, >Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. unam.