Re: [gmx-users] GTX 960 vs Tesla K40

Hi, Regarding the K40 vs GTX 960 question, the K40 will likely be a bit faster (though it'l consume more power if that matters). The difference will be at most 20% in total performance, I think -- and with small systems likely negligible (as a smaller card with higher clocks is more efficient at

Re: [gmx-users] conversion issue from .str to .itp

On 6/15/18 10:39 AM, abhisek Mondal wrote: Hi, I'm facing an issue converting nap.str into nap.itp. I used nap.mol2 file in CGenFF server to get the nap.str file. However when I use the following command to convert, I get the following error: python cgenff_charmm2gmx.py NAP NAP_Hadded.mol2

[gmx-users] conversion issue from .str to .itp

Hi, I'm facing an issue converting nap.str into nap.itp. I used nap.mol2 file in CGenFF server to get the nap.str file. However when I use the following command to convert, I get the following error: python cgenff_charmm2gmx.py NAP NAP_Hadded.mol2 nap2.str charmm36.ff Error: NOTE1: Code tested

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

On 6/14/18 4:01 AM, Own 12121325 wrote: Hello, I wonder to know if it's necessary to provide edr file for the completed part of the simulation in order to continue the md job assuming that I provide the trajectory (with coordinates and velocities) using gmx convert-tpr. Does the ensembles

[gmx-users] Protein-surface Binding energy

Dear Gromacs users, I have a question regarding the calculation of binding energy for protein-surface interactions. I found that for protein-ligand systems, LIE method was suggested but what about protein-surface? if I have done two simulations, one with protein attached to the surface and the

[gmx-users] Error in -rerun

Dear All, As I have specified in my earlier mail, I wanted to know which input trajectory has to be supplied to -rerun flag in mdrun for recalculation of electrostatic energies between protein-solvent from gromacs (as proposed by Lindgren et al, in the paper "On the stability of chymotrypsin

[gmx-users] Compilation issue, MacOS 10.13.5 - Gromacs 2018 - CUDA 9.2

Hi, I’m struggling to install Gormacs 2018 on my MacBook pro (late 2013) with cuda support for the NVIDIA GeForce GT 750M. I’m using Clang-6.0 installed with macports for OpenMP support, and clang from Xcode 9.2 for support of cuda 9.2 and cmake stage is fine using : cmake .. -DGMX_GPU=ON

Re: [gmx-users] Regarding the code for HB auto-correlation function code

Den 2018-06-15 kl. 07:39, skrev Dilip.H.N: Sir, I have done the simulation of amino-acid+water+cosolvents in GROMACS and now i want to calculate the HB auto-correlation functions.In GROMACS there is only intermittent HB and not Continuous HB. And hence i am trying with MDAnalysis which is a