[gmx-users] Running Gromacs on GPUs

Dear Gromacs users, I am trying to run a multiple walkers metadynamics simulation on Gromacs 5.1.4 using a machine that has 12 CPUs and 4 GPUs. I have compiled Gromacs using the following schems: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on -DGMX_GPU=on -DGMX_USE_OPE

[gmx-users] Fwd: monitor the size of the computational box

Dear all, I would like to ask what is the best way to monitor the size of the computational box (i.e. the volume) during a simulation. I know that it must stay constant during the simulation but, in my case, it seems that it doesn't. There is an error poping up when I try to use the gmx hbond tool

[gmx-users] monitor the size of the computational box

Dear all, I would like to ask what is the best way to monitor the size of the computational box (i.e. the volume) during a simulation. I know that it must stay constant during the simulation but, in my case, it seems that it doesn't. There is an error poping up when I try to use the gmx hbond tool

[gmx-users] trjcat issue

Dear all, I tried to concatenate two trajectories using the comand trjcat -f Trajectory_total.xtc md26_out.xtc -o Trajectory_total_full.xtc The process ended normaly: Reading frame 1 time 3000310.000 Summary of files and start times used: FileStart time Ti

[gmx-users] make_ndx question

Dear all, I am very amateur in GROMACS, so please forgive my silly question. I want to group the following atoms ATOM 2285b C1 LIG X 6 32.880 59.958 110.850 0.00 0.00 ATOM 2285c CL1 LIG X 6 31.972 61.400 110.520 0.00 0.00 ATOM 2285d N1 LIG X 6 32.318 58.744 110.53

[gmx-users] Index file

Dear all, I am very amateur in GROMACS, so please forgive my silly question. I want to group the following atoms ATOM 2285b C1 LIG X 6 32.880 59.958 110.850 0.00 0.00 ATOM 2285c CL1 LIG X 6 31.972 61.400 110.520 0.00 0.00 ATOM 2285d N1 LIG X 6 32.318 58.744 110.53