[gmx-users] Number of ligand contacts over the trajectories

Dear Gromacs users, I am working with protein-ligand interaction. I would like to calculate the number of contacts ligand make with the protein within a specific cut off ( say within 3.5 to 4.5 angstroms), along the simulation trajectories. Is there any Gromacs analysis script, which can help me w

Re: [gmx-users] DSSP problem

Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l total 92332632 -rw-rw-r-- 1 Mass Mass 0 Sep 8 19:46 310Helix.dat -rw--- 1 Mass Mass 371878 Aug 21 07:39 3BLG_115XrayWater.top -rw-rw-r-- 1 Mass M

[gmx-users] Gromacs on Stampede

Why not put it in a slurm script and submit that script as a (probably single-node) job. It is not generally acceptable to use a large fraction of the head node of a shared resource for a substantial amount of time. If your problem is different and of a gromacs nature, you may need to describe

Re: [gmx-users] energy drift - comparison of double and single precision

On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot < guillaume.chev...@gmail.com> wrote: > 2013/10/12 Mark Abraham > > > Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) > > 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger > than > > that. I bet the r