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.
-Justin
Please suggest.
Thanks in advance.
Samrat
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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