Re: [gmx-users] simulation on 2 gpus

Hi, I've done a lot of research/experimentation on this, so I can maybe get you started - if anyone has any questions about the essay to follow, feel free to email me personally, and I'll link it to the email thread if it ends up being pertinent. First, there's some more internet resources to

Re: [gmx-users] gmx insert-molecules question

Thanks! (and sorry about all the typos in my original email -- just re-read it and saw it was barely intelligible!) M On Thu, Jul 25, 2019 at 4:25 PM Justin Lemkul wrote: > > > On 7/25/19 4:11 PM, Mala L Radhakrishnan wrote: > > Hi, > > > > I am trying to crod snapshots with multiple copies

Re: [gmx-users] gmx insert-molecules question

On 7/25/19 4:11 PM, Mala L Radhakrishnan wrote: Hi, I am trying to crod snapshots with multiple copies of a molecule. When I run gmx insert-molecules and I have a box of a certain size, does it make sure that there is no overlap of molecules even considering pbc? What I mean by this is if

Re: [gmx-users] Angular distribution

On 7/25/19 8:05 AM, Omkar Singh wrote: Hi everyone, I have a protein Water simulated system and I want to calculate Angular distribution function. How can I find can anyone help me with this? What angles do you want to calculate? -Justin --

[gmx-users] gmx insert-molecules question

Hi, I am trying to crod snapshots with multiple copies of a molecule. When I run gmx insert-molecules and I have a box of a certain size, does it make sure that there is no overlap of molecules even considering pbc? What I mean by this is if I do a trjconv on the resulting crowded snapshot,

[gmx-users] simulation on 2 gpus

Dear all, I am trying to run simulation with Gromacs 2019.2 on a workstation with an amd Threadripper cpu (32 core, 64 threads, 128 GB RAM and with two rtx 2080 ti with nvlink bridge. I read user's guide section regarding performance and I am exploring some possibile combinations of cpu/gpu work

[gmx-users] Angular distribution

Hi everyone, I have a protein Water simulated system and I want to calculate Angular distribution function. How can I find can anyone help me with this? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Sun Solaris

On Thu, Jul 25, 2019 at 11:31 AM amitabh jayaswal wrote: > > Dear All, > *Namaskar!* > Can GROMACS be installed and run on a Sun Solaris system? Hi, As long as you have modern C++ compilers and toolchain, you should be able to do so. > We have a robust IBM Desktop which we intend to

[gmx-users] Sun Solaris

Dear All, *Namaskar!* Can GROMACS be installed and run on a Sun Solaris system? We have a robust IBM Desktop which we intend to dedicatedly use for GROMACS; however we are facing difficulties in installing it. The machine specifications are: PRODUCT NAME: IBM System x3400 MACHINE TYPE: 7973

Re: [gmx-users] remd error

This is an MPI / job scheduler error: you are requesting 2 nodes with 20 processes per node (=40 total), but starting 80 ranks. -- Szilárd On Thu, Jul 18, 2019 at 8:33 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > > Hi, >I am running remd simulation in gromacs-2016.5. After

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Hi, It is not clear to me how are you trying to set up your runs, so please provide some details: - are you trying to run multiple simulations concurrently on the same node or are you trying to strong-scale? - what are you simulating? - can you provide log files of the runs? Cheers, -- Szilárd

[gmx-users] older server CPUs with recent GPUs for GROMACS

Hi Mike, Forking the discussion to have a consistent topic that is more discoverable. On Thu, Jul 18, 2019 at 4:21 PM Michael Williams wrote: > > Hi Szilárd, > > Thanks for the interesting observations on recent hardware. I was wondering > if you could comment on the use of somewhat older