[gmx-users] gro file format /pulling

aherz alexander.herz at mytum.de
Mon Aug 31 18:35:48 CEST 2009


I'm pulling 2 diamond slabs (which enclose two water slabs) in opposite
with pull_rate1=0.01 (nm/ps) in x direction (pbc in 3d).
Now looking at the gro file that is finally output when the sim is
finshied and averaging
the speeds of the two diamonds I get ca. +/-1.78 (I guess  [nm/ps])
(different signs cause the
diamond slabs are pulled in opposite direction). Looking at the
trajectory, the pulling
looks ok (so the diamonds have ca. const speed in opposite direction).

Now, is the speed I get from the gro file actually in nm/ps and how does
it relate to my
0.01 nm/ps pull_rate1 (shouldn't it be ca. 0.01 nm/ps)??

Here is the pull setup:
pull            = umbrella
pull_geometry   = direction
pull_ngroups         = 1
pull_group0          = DIAM
pull_group1          = DIAM2
pulldim         = Y Y Y
pull_k1          = 1000.0
pull_rate1       = 0.01
pull_vec1        = -1.0 0.0 0.0

More information about the gromacs.org_gmx-users mailing list