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

Samrat Pal psamrat10 at yahoo.com
Tue Nov 16 02:09:27 CET 2010

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? 

Please suggest.

Thanks in advance.


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