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

Samrat Pal 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 
pulling simulation

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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