[gmx-users] Subject: Re: how to avoid multiple 'aprun' on batch job script?

Thank you Justin, indeed wallclock limit is there, there are heterogeneity on performance (40 ns to 120 ns for 24:00:00) also and to avoid the very large trr file we do follow the smaller bin. One need to submit few time same job. Regarding heterogeneity: in order to balance PP:PME load imbalance

[gmx-users] [pairs] directive issue

Dear Users, I am introducing a new ff for a small molecule in the Amber forcefield , I have itp file for the new molecule ( by antechamber ) and uses RB potential for proper dihedrals and so tried to copy and paste [ pairs ] directive from itp file to ffbonded.itp but grompp run reports invalid dir

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

On Fri, May 8, 2015 at 8:44 PM, Malcolm Tobias wrote: > > Szilárd, > > On Friday 08 May 2015 20:25:09 Szilárd Páll wrote: >> > I wouldn't expect the CPUSETs to be problematic, I've been using them with >> > Gromacs for over a decade now ;-) >> >> Thread affinity setting within mdrun has been empl

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Szilárd, On Friday 08 May 2015 20:25:09 Szilárd Páll wrote: > > I wouldn't expect the CPUSETs to be problematic, I've been using them with > > Gromacs for over a decade now ;-) > > Thread affinity setting within mdrun has been employed since v4.6 and > we do it on a per-thread basis and not doi

Re: [gmx-users] 35% Variability in Simulation Performance

Brief comments/tips, I hope I did not miss essential parts of the previous discussion :) First of all, performance consistency on Cray's Gemini network is known to be affected by job placement - that'y why Blue Waters has a locality-aware scheduler which can place jobs reasonably compact/contiguou

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

On Fri, May 8, 2015 at 4:45 PM, Malcolm Tobias wrote: > > Szilárd, > > On Friday 08 May 2015 15:56:12 Szilárd Páll wrote: >> What's being utilized vs what's being started are different things. If >> you don't believe the mdrun output - which is quite likely not wrong >> about the 2 ranks x 4 threa

Re: [gmx-users] Gas phase simulation

Thanks a lot for your suggestions Chris. I will try them and share the results with you. Bests On Thu, May 7, 2015 at 12:24 AM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > As a debugging method, I'd suggest to try pulling out the other side, from > water directly into vacuum. I ha

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

On Fri, May 8, 2015 at 4:28 PM Malcolm Tobias wrote: > > Mark, > > On Friday 08 May 2015 13:48:30 Mark Abraham wrote: > > > What kind of simulation are you testing with? A reaction-field water box > > will have almost nothing to do on the CPU, so no real change with > #threads. > > Check with you

Re: [gmx-users] rerun under non-bonded E. terms

Thanks for being so quick. Cheers, Albert On 05/08/2015 03:44 PM, Justin Lemkul wrote: On 5/8/15 10:43 AM, Albert Solernou wrote: Thanks Justin, by removing all the bonded terms from the topology you mean edit "topol_Protein_chain_A.itp" and remove the sections "bonds", "pairs", "angles", an

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Szilárd, On Friday 08 May 2015 15:56:12 Szilárd Páll wrote: > What's being utilized vs what's being started are different things. If > you don't believe the mdrun output - which is quite likely not wrong > about the 2 ranks x 4 threads -, use your favorite tool to check the > number of ranks and

Re: [gmx-users] rerun under non-bonded E. terms

On 5/8/15 10:43 AM, Albert Solernou wrote: Thanks Justin, by removing all the bonded terms from the topology you mean edit "topol_Protein_chain_A.itp" and remove the sections "bonds", "pairs", "angles", and "dihedrals"? Yes, but of course this renders the topology nonfunctional, so make sur

Re: [gmx-users] rerun under non-bonded E. terms

Thanks Justin, by removing all the bonded terms from the topology you mean edit "topol_Protein_chain_A.itp" and remove the sections "bonds", "pairs", "angles", and "dihedrals"? Cheers, Albert On 05/08/2015 03:35 PM, Justin Lemkul wrote: On 5/8/15 10:25 AM, Albert Solernou wrote: Hi All, i

Re: [gmx-users] rerun under non-bonded E. terms

On 5/8/15 10:25 AM, Albert Solernou wrote: Hi All, is there a way to do a re-run using only non-bonded energy terms? Remove all bonded terms from the topology, re-create a .tpr, and re-run. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirsc

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Mark, On Friday 08 May 2015 13:48:30 Mark Abraham wrote: > What kind of simulation are you testing with? A reaction-field water box > will have almost nothing to do on the CPU, so no real change with #threads. > Check with your users, but a PME test case is often more appropriate. I have no ide

[gmx-users] rerun under non-bonded E. terms

Hi All, is there a way to do a re-run using only non-bonded energy terms? Cheers, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Gromacs Users mailing list * Pl

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

On Fri, May 8, 2015 at 2:50 PM, Malcolm Tobias wrote: > > Hi Mark, > > On Friday 08 May 2015 11:51:03 Mark Abraham wrote: >> > >> > I'm attempting to build gromacs on a new cluster and following the same >> > recipies that I've used in the past, but encountering a strange behavior: >> > It claims

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Hi, On Fri, May 8, 2015 at 3:01 PM Malcolm Tobias wrote: > > Hi Mark, > > On Friday 08 May 2015 11:51:03 Mark Abraham wrote: > > > > > > I'm attempting to build gromacs on a new cluster and following the same > > > recipies that I've used in the past, but encountering a strange > behavior: > > >

[gmx-users] adding -qstep to g_saxs

Dear all, I wonder if anybody had ever tried to add a similar function of "-qstep" in g_sans into g_saxs, or ever tried to modify g_sans into a more functional g_saxs? I used g_saxs to calculate SAXS curves with q varied from 0 to 1 (1/nm) in order to compare with experiment, but I only got ten d

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Hi Mark, On Friday 08 May 2015 11:51:03 Mark Abraham wrote: > > > > I'm attempting to build gromacs on a new cluster and following the same > > recipies that I've used in the past, but encountering a strange behavior: > > It claims to be using both MPI and OpenMP, but I can see by 'top' and the >

Re: [gmx-users] Gromacs 4.6.7 with MPI and OpenMP

Hi, On Thu, May 7, 2015 at 6:16 PM Malcolm Tobias wrote: > > All, > > I'm attempting to build gromacs on a new cluster and following the same > recipies that I've used in the past, but encountering a strange behavior: > It claims to be using both MPI and OpenMP, but I can see by 'top' and the >

Re: [gmx-users] how to avoid multiple 'aprun' on batch job script?

On 5/8/15 1:31 AM, Satyabrata Das wrote: Dear All, Currently I am running simulation using Gromac-5.0.4 on Cray XC40. Its a protein in water system (100K), 300K, NPT ensemble, writing full precision output in every 2ps and compressed trajectory in 1ps. I have divided the run into 2ns bin, and

[gmx-users] mail about g_select tool

Dear Justin thank you for your reply    I  wish to peculiarly select SOL  molecules within 0.7 nm from  the surface of CNT  to find dipole moment fluctuation  of those molecules . here i wish to choose g_select tool to get output index (-on) fil

Re: [gmx-users] Distance Restraints

Dear Steve, First of all you should take a look in all mdp options regarding distance restraints: http://manual.gromacs.org/archive/4.5/online/mdp_opt.html#nmr I am not 100% familiar with dist res in version 4.5.4 but without "dirse=simple" for example I think you will not have any distance restra