[gmx-users] compressing two selections or just the reverse of pulling simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 16 03:16:51 CET 2010

Samrat Pal wrote:
> Hi All,
>            In general what we do in pulling simulations that we pull one 
> selection keeping the other fixed. In that case the distance between the 
> two selections increases with time. Now, I want to push the selections 
> i.e. one selection will be kept fixed and the other will be pushed 
> towards the fixed one so that the distance between the two selection 
> will decrease. Is it possible to do that in GROMACS? What should I 
> modify in the mdp file? I am attaching a mdp file that I have used for 
> pulling simulations (only the pull part).
> ; pull code
> pull = umbrella
> pull_geometry = distance
> pull_dim = N N Y
> pull_start = yes
> pull_ngroups = 1
> pull_group0 = freeze
> pull_group1 = pull
> pull_rate1 = 0.01
> pull_k1 = 1000
> I have used pull_dim N N Y as I am interested to pull only in the z 
> direction. Should I just use N N -Y to do the compressing simulations?

You can't specify "negative yes" for a pulling direction.  Instead, just set the 
pull rate to, i.e., -0.01 to pull in the opposite direction.


> Please suggest.
> Thanks in advance.
> Samrat


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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