Re: [gmx-users] viscosity calculation using g_energy

Hello David, I have the same problem I run the simulation for 10 ns and I saved energies every 1 ps but the results were far and the curves go to negative values. Please, do have an idea how to get accurate results? Thank you Ali On Thu, Apr 5, 2018 at 2:12 PM, David van der Spoel

Re: [gmx-users] anyone have a development version or fork of gromacs that puts bonded interactions on the GPUs?

Dear Kevin: Perhaps I misstated my goals. I am not saying that GPUs don't ever help. I am saying that Martini simulations with GPUs should be really heavily cpu-bound with bonded interactions, once an afterthought, now a dominant factor in determining throughput. Therefore, martini

Re: [gmx-users] anyone have a development version or fork of gromacs that puts bonded interactions on the GPUs?

Hi Chris, My experience has been that GPUs do significantly increase performance in Martini simulations, perhaps not quite as much as all-atom simulations but typically at least ~2x the speed of the same system on cpus alone. What combination of gromacs version/mdp options/hardware are you

Re: [gmx-users] Regarding calculation of Spatial Distribution Function

Mark addressed your second post. Regarding your first post, it looks like that program help output was mangled somewhere between 4.6.5 and 5.1.2. Below is the output from g_spatial in gromacs 4.6.5, which should give you an idea of what the help output should say (e.g. use a .xtc input file and

Re: [gmx-users] viscosity calculation using g_energy

Den 2018-04-05 kl. 09:19, skrev Jo: Hello, I would like to calculate bulk and shear viscosity on gromacs using g_energy. I have read a number of other emails about this topic but there still seems to be no conclusive answer to how to use this tool. I use the following command: gmx energy -f

[gmx-users] anyone have a development version or fork of gromacs that puts bonded interactions on the GPUs?

Hello, running Martini simulations with gromacs does not dramatically benefit from the presence of GPUs, presumably because the bonded interactions on the CPUs is the bottleneck. Does anyone have even an untested hacky version of gromacs with bonded pushed to the GPUs? PME is not used so that

[gmx-users] Problem with CUDA

Hello. I'm taking a working build from a co-worker and trying to add GPU support on a Cray XC. CMake works but make fails. Both 2016 and 2018 die at the same point -- can't find gromac's own routines. 2016.5: /opt/cray/pe/craype/2.5.13/bin/CC-march=core-avx2 -O2 -fPIC -dynamic -std=c++0x

[gmx-users] charmm-gui

Dear Justin,Can I use the charmm-gui output file for peptide (.itp file) as an input file for GROMACS, and instead of one peptide, I set 4 peptides in the bulk of water and near the head groups?In fact , I want to extract manually peptide from the final .gro file containing peptide + lipids +

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

Am 03.04.18 um 19:03 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 5:10 PM, Jochen Hub wrote: Am 03.04.18 um 16:26 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub wrote: benchmar Am 29.03.18 um 20:57 schrieb Szilárd Páll: Hi Jochen, For

[gmx-users] viscosity calculation using g_energy

Hello, I would like to calculate bulk and shear viscosity on gromacs using g_energy. I have read a number of other emails about this topic but there still seems to be no conclusive answer to how to use this tool. I use the following command: gmx energy -f prod_500.edr -vis viscosity.xvg