Re: [gmx-users] Gmx gangle

On Wed, 12 Dec 2018, 02:03 Mark Abraham Hi, > > I would check the documentation of gmx gangle for how it works, > particularly for how to define a plane. Thank you so much Mark. As a GROMACS lover, I like to make a suggestion; I think sth it would be REALLY helpful if you provide some proper

Re: [gmx-users] using dual CPU's

Hi, In your case the slow down was in part because with a single GPU the PME work by default went to that GPU. But with two GPUs the default is to leave the PME work on the CPU (which for your test was very weak), because the alternative is often not a good idea. You can try it out with the

Re: [gmx-users] using dual CPU's

Szilard, Thank you vey much for the information and I apologize how the text appeared - internet demons at work. The computer described in the log files is a basic test rig which we use to iron out models. The workhorse is a many core AMD with now one and hopefully soon to be two 2080ti’s,

Re: [gmx-users] Gmx gangle

Hi, I would check the documentation of gmx gangle for how it works, particularly for how to define a plane. Also, 4.5.4 is prehistoric, please do yourself a favor and use a version with the seven years of improvements since then :-) Mark On Tue., 11 Dec. 2018, 10:14 rose rahmani, wrote: > Hi,

Re: [gmx-users] Domain decomposition and large molecules

Hi, Unfortunately, you can't attach files to the mailing list. Please use a file sharing service and share the link. Mark On Wed., 12 Dec. 2018, 02:20 Tommaso D'Agostino, wrote: > Dear all, > > I have a system of 27000 atoms, that I am simulating on both local and > Marconi-KNL (cineca)

Re: [gmx-users] Install GROMACS 2018 with CUDA features in dynamic linking way

AFAIK the right way to control RPATH using cmake is: https://cmake.org/cmake/help/v3.12/variable/CMAKE_SKIP_RPATH.html no need to poke the binary. If you still need to turn off static cudart linking the way to do that is also via a CMake feature:

Re: [gmx-users] using dual CPU's

Without having read all details (partly due to the hard to read log files), what I can certainly recommend is: unless you really need to, avoid running single simulations with only a few 10s of thousands of atoms across multiple GPUs. You'll be _much_ better off using your limited resources by

[gmx-users] Area compressibility modulus GMX

Hi all, I have a weird, probably very basic question to ask and I hope it is appropriate for the mailing list. I am trying to reproduce the pure DPPC bilayer data found in J. Chem. Theory Comput., 2016, 12 (1), pp 405–413 (10.1021/acs.jctc.5b00935) using the recommended protocol given in the

[gmx-users] Domain decomposition and large molecules

Dear all, I have a system of 27000 atoms, that I am simulating on both local and Marconi-KNL (cineca) clusters. In this system, I simulate a small molecule that has a graphene sheet attached to it, surrounded by water. I have already simulated with success this molecule in a system of 6500 atoms,

Re: [gmx-users] download GROMOS54a6oxy

Hi Tushar, all parameters from GROMOS 53A6_OXY along with other improvements have been merged into a new parameter set called 2016H66 (see https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00187). Philippe Hünenberger put some files for GROMACS on his website:

Re: [gmx-users] Install GROMACS 2018 with CUDA features in dynamic linking way

I'm trying to rewrite the RPATH because shared libraries paths used by GROMACS are hardcoded in the binary. ldd /nfs2/opt/APPS/x86_64/APPS/GROMACS/2016/CUDA/8.0/bin/gmx linux-vdso.so.1 => (0x7ffddf1d3000) libgromacs.so.2 =>