Re: [gmx-users] several runs

Hi, The interference is just that the runs will be ridiculously slow. You want either to arrange life to run one simulation at a time, or manually allocate cores to separate simulations, e.g. as described at

Re: [gmx-users] several runs

Hi Justin, Thank you for your answer! If you may help with any of these questions I would be greatly grateful; How can I understand if they were interfered? How is pinning? Any other ways you can recommend? Thanks a lot On Tue, Feb 24, 2015 at 10:14 PM, mah maz mahma...@gmail.com wrote: Is

Re: [gmx-users] Computing Resource - Laptop

Sorry I meant desktop, laptop must have been a mental error as I'm looking for a new personal laptop. -Douglas Grahame -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Szilárd Páll Sent:

Re: [gmx-users] several runs

mdrun -multi works too if the runs are identical. Or write your own bash wrapper that calculates thread counts and applies pin offsets manually (see the link Mark posted for pinning info). -- Szilárd On Tue, Feb 24, 2015 at 8:40 PM, mah maz mahma...@gmail.com wrote: Hi Justin, Thank you for

Re: [gmx-users] several runs

Perhaps I can be of help here. Except for the smallest systems, GROMACS simulations are very compute-intensive, so a single machine is needed for a single job. In many instances, several machines are required for a single job (provided you have a fast enough network). If you give a single

Re: [gmx-users] Doubt about energies in a very simple system

Hi, In addition to Justin's points about comparing apples with apples on the same coordinates, by default in the Verlet scheme GROMACS also shifts the potential to be zero at the cutoff, so that the potential is actually the integral of the force (mentioned in manual 3.4.2, along with a sea of

Re: [gmx-users] Doubt about energies in a very simple system

Hi Justin, I always do the SPE as follows: grompp -f SPE.mdp -p sys.top -c sys.gro and after that I simply execute mdrun, i didn't know about the mdrun -rerun function. Now I have done: mdrun -s topol.tpr -rerun sys.gro but the energy results are the exactly the same. Thank you. 2015-02-24

Re: [gmx-users] On the collective dynamics in terms of NMA and PCA

Hi James, Imagine you have a landscape with a long valley, longer than it's broad. Now you go to the deepest point and determine the shallowest direction. Then you take the shallowest direction perpendicular to the first. That's NMA. Now you stand before the valley, and you roll a big ball down,

[gmx-users] Application of electric field on membrane

Dear Developers,I am new to GromacsI have installed Gromacs4.5.5. I have tried the membrane tutorial..I want to apply intense pulsed electric field with 100ps rise time...How do i run the simulation.Have to modify md.mdp file before production md simulation,,,Kindly help me to run the

Re: [gmx-users] Gromacs in windows 7 with GPU

On 24.02.2015 05:08, 라지브간디 wrote: I have a Windows 7 OS system which has i7, CPU @ 3.40GHz, 16 GB RAM and newly installed NVIDIA GeForce GX960 with 1 TB memory. Since i am familiar with gromacs in Linux system, i am not able to install in windows environment. Should i use cygwin or Visual

Re: [gmx-users] On the collective dynamics in terms of NMA and PCA

Hi Tsjerk, thank you very much for the explanation! So in that case the choosing of the best method in relation to specified task will depend on the sensitivity of both methods. In case of NMA it should be based on the knowing that initial structure is lied within the deepest minima along all

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

Hey Harry, Thanks for the caveat. Carsten Kutzner posted these results a few days ago. This is what he said : I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24 ns/d on 64 AMD cores 6272 16 ns/d on 32 AMD cores 6380 36 ns/d on

Re: [gmx-users] On the collective dynamics in terms of NMA and PCA

Oh, there's a minor correction to NMA. You actually determine the steepest gradient first, and then the steepest gradient perpendicular to the first direction. That's why the smallest normal modes correspond to the largest eigenvectors :) Cheers, Tsjerk On Tue, Feb 24, 2015 at 11:31 AM, Tsjerk

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

Hi Szilard, Thank you very much for your great advice. 2015-02-20 19:03 GMT+01:00 Szilárd Páll pall.szil...@gmail.com: On Fri, Feb 20, 2015 at 2:17 PM, David McGiven davidmcgiv...@gmail.com wrote: Dear Gromacs users and developers, We are thinking about buying a new cluster of ten or

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

BSD Dear David, Hey Harry, Thanks for the caveat. Carsten Kutzner posted these results a few days ago. This is what he said : I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24 ns/d on 64 AMD cores 6272 16 ns/d on 32 AMD cores

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

2015-02-24 15:46 GMT+01:00 Szilárd Páll pall.szil...@gmail.com: Perhaps he has seen some real results that do not show issues at 16 or 18 cores/socket, in which case they would be advantageous, if one can afford them. I am only going on what the manager of our cluster mentioned to me in

[gmx-users] Announcement: release of FESetup 1.1

Dear Gromacs community, We are pleased to announce the release of FESetup 1.1. FESetup is a tool to automate setup of alchemical relative free energy simulations like thermodynamic integration (TI) and can also be used for general simulation setup (equilibration). The tool will automatically

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

Le 24/02/2015 13:29, David McGiven a écrit : I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24 ns/d on 64 AMD cores 6272 16 ns/d on 32 AMD cores 6380 36 ns/d on 32 AMD cores 6380 with 1x GTX 980 40 ns/d on 32 AMD cores 6380

Re: [gmx-users] g_rdf

Dear Justin, Thanks. I have another question about coordination number ( the cumulative number ). I am looking for RDF between two type of atoms, first is Ca ions and the second group is Oxygen of side chains of peptide at solid/liquid interfaces. I don't understand the integration of RDF. I

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

On Tue, Feb 24, 2015 at 2:09 PM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear David, Hey Harry, Thanks for the caveat. Carsten Kutzner posted these results a few days ago. This is what he said : I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms

[gmx-users] modified residues and residual charge

BSD Dear All, I was wondering how people deal with the issue of generating special amino acids in Gaussian, then being left with residual charge upon removing blocking blocks. The process I follow is: 1. Build the modified amino acid (side chain is non-standard) in Gaussian, with

[gmx-users] How to perform simulation between initial and final structures

Dear All, I am working in a GTPase protein and I have two PDB structures of my protein in GTP-bound and GDP-bound state which have two different conformations. Now I want to perform simulation in between the structures to see how the conformational change is taking place. So is it possible

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

On Tue, Feb 24, 2015 at 12:32 PM, David McGiven davidmcgiv...@gmail.com wrote: Hi Szilard, Thank you very much for your great advice. 2015-02-20 19:03 GMT+01:00 Szilárd Páll pall.szil...@gmail.com: On Fri, Feb 20, 2015 at 2:17 PM, David McGiven davidmcgiv...@gmail.com wrote: Dear Gromacs

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

On 2/24/15 8:09 AM, Harry Mark Greenblatt wrote: BSD Dear David, Hey Harry, Thanks for the caveat. Carsten Kutzner posted these results a few days ago. This is what he said : I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

On Tue, Feb 24, 2015 at 1:17 PM, Harry Mark Greenblatt harry.greenbl...@weizmann.ac.il wrote: BSD Dear David, We did some tests with Gromacs and other programs on CPU's with core counts up to 16 per socket, and found that after about 12 cores jobs/threads begin to interfere with each

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

On Tue, Feb 24, 2015 at 3:44 PM, Téletchéa Stéphane stephane.teletc...@univ-nantes.fr wrote: Le 24/02/2015 13:29, David McGiven a écrit : I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24 ns/d on 64 AMD cores 6272 16 ns/d on 32

[gmx-users] Doubt about energies in a very simple system

Hi, I designed a very simple system that is composed of only one Glutamine with Tleap. I've transformed the corresponding .prmtop and .inpcrd into .top and .gro files, using a conversor that I'm developing. I attach .top .gro and .mdp files [ defaults ] ; nbfunccomb-rule

Re: [gmx-users] several runs

Is running simulations in several terminals problematic? On Tue, Feb 24, 2015 at 8:42 PM, mah maz mahma...@gmail.com wrote: Dear all, How can I perform several simulations simultaneously (in linux)? thank you! -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] several runs

On 2/24/15 1:44 PM, mah maz wrote: Is running simulations in several terminals problematic? Usually. Unless you keep them from interfering with each other with pinning, the performance will degrade badly. Though if you're doing multiple runs on a normal desktop, performance isn't going

[gmx-users] several runs

Dear all, How can I perform several simulations simultaneously (in linux)? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

Re: [gmx-users] Application of electric field on membrane

On 2015-02-24 10:26, petrishia petrishia wrote: Dear Developers,I am new to GromacsI have installed Gromacs4.5.5. I have tried the membrane tutorial..I want to apply intense pulsed electric field with 100ps rise time...How do i run the simulation.Have to modify md.mdp file before

Re: [gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

Le 24/02/2015 17:18, Szilárd Páll a écrit : Thanks! Let me note that those observations are particular to your machine. There are multiple factors that cumulatively affect the multi-threaded scaling: - physical vs HT threads - crossing socket boundaries - iteration time/data per thread - GPU and

[gmx-users] Computing Resource - Laptop

Hey everyone I'm not sure if this is the place to post this or not so my apologies if it is not. Our lab recently got some funds to put towards a desktop for molecular dynamics work and we have a budget of aprx. $4,000 CDN for the laptop. Given that I am not an expert in the hardware area, nor do

[gmx-users] GROMOS vs. CHARMM dihedrals

Hi all, I was wondering about interchangeability of proper dihedral parameters between GROMOS and CHARMM force fields. I am building a new, non-proteic residue, and I would like to use parameters from my GROMOS structure for the CHARMM simulation. Specifically, I would like to use the proper

Re: [gmx-users] GROMOS vs. CHARMM dihedrals

On 2/24/15 1:19 PM, Bianca Villavicencio wrote: Hi all, I was wondering about interchangeability of proper dihedral parameters between GROMOS and CHARMM force fields. I am building a new, non-proteic residue, and I would like to use parameters from my GROMOS structure for the CHARMM

Re: [gmx-users] Energy minimization for Inositol pyrophosphate

Hello, I have understood my mistakes that I reported in previous queries of this string. now, I am proceeding more systematically. I have generated ff parameters for Inositol Pyrophosphate with the help of PRODRG server (as mentioned in the tutorials) as a residue and added it to

Re: [gmx-users] several runs

Dear Mark,Victor,Szilard So many thanks for your helpful comments! Cheers On Tue, Feb 24, 2015 at 11:10 PM, mah maz mahma...@gmail.com wrote: Hi Justin, Thank you for your answer! If you may help with any of these questions I would be greatly grateful; How can I understand if they were

Re: [gmx-users] several runs

On Tue, Feb 24, 2015 at 10:54 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: Perhaps I can be of help here. Except for the smallest systems, GROMACS simulations are very compute-intensive, so a single machine is needed for a single job. In many instances, several machines are required

Re: [gmx-users] Umbrella Sampling Dissociation Constant

Error in equation, see the equation at the bottom of this wiki page: http://en.wikipedia.org/wiki/Binding_constant From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Alexander Law

[gmx-users] Umbrella Sampling Dissociation Constant

Is it possible to use the Gibbs free energy value produced from an umbrella sampling experiment to calculate the dissociation constant? The PMF difference between the energy minimum to the plateau region is -18 kcal mol-1 what is the Kd value? Is the following equation applicable?: Kd

Re: [gmx-users] Computing Resource - Laptop

How many? What kind of simulations and analysis (asking to know if you'll need many cores, fewfast cores, GPUs, etc.)? 4000 CAD is a quite decent sum, it should get you at least 2 fast workstations. -- Szilárd On Tue, Feb 24, 2015 at 9:36 PM, Douglas Grahame dgrah...@uoguelph.ca wrote: Sorry

Re: [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS

Dear gmx-users, Ok Justin here is the information you asked for: See Figure 3 for the antimcirobial bacterial-type membrane disruption models that the antimicrobial peptide maximin 3 might be using.  Note that all models require the interaction of several maximin 3 molecules not just one