[gmx-users] compressing two selections or just the reverse of pulling simulation
psamrat10 at yahoo.com
Tue Nov 16 20:07:33 CET 2010
Oh! Thanks a lot.
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Mon, November 15, 2010 6:16:51 PM
Subject: Re: [gmx-users] compressing two selections or just the reverse of
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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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