[gmx-users] simulations in parallel using the pull code

Dear Gromacs community, I modified the pull code in GROMACS to apply forces on atoms that are in a certain region of space. It compiles error free and runs fine to give me the expected results. I then recompiled with mpi support. The cluster I am using has 8 cores/processors per node. When

[gmx-users] follow up: simulations in parallel using the pull code

coupling. I have left a vapor layer of a few nanometers to allow for any density changes. I hope this further information helps in debugging. Thanks Sumanth Jamadagni Dear Gromacs community, I modified the pull code in GROMACS to apply forces on atoms that are in a certain region of space. It

[gmx-users] Semi-isotropic pressure coupling

Hi, I was performing NPT simulation of a water - solid interface and used Berendsen Semi-Isotropic coupling. The solid is a SAM - 11 atoms long and packed together closely to form a surface in the x-y plane. Pcoupl = Berendsen Pcoupltype = semiisotropic;

[gmx-users] Simulations backward in time.

Hi, I wanted to perform some simulations backward and forward in time (for transition path sampling ). If I specify a negative value for 'dt' in the mdp file, would that work for backward integration of the equations of motion ? Thanks Sumanth N Jamadagni Graduate Student Isermann Dept of

[gmx-users] simulations backward in time

Using a negative 'dt' in the mdp file does not not seem to cause any simulation problems (tested on a waterbox- doesn't crash). I am not sure if the system is evolving backwards in time though. I am not sure how to check that. But I think, all I require is that the equations of motion be integr