[gmx-users] Pulling

asasa qsqs sanaz_dr_m at yahoo.com
Thu Dec 25 20:51:48 CET 2014

Dear Justin A. Lemkul,
> I want to use pulling code for calculate the PMF of a molecule at the across the
> DMPC, but i can't obtained a large pull across the membrane my pulling code was:
> ; Pull code
> pull= umbrella
> pull_geometry= position
> pull_dim= N N Y
> pull_start = yes                ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0= DMPC
> pull_group1= QBH
> pull_k1= 1000                  ; kJ mol^-1 nm^-2
> pull_vec1= 0 0 0.5
> after  "perl distances.pl" step i obtained a summary.dat file. but in this file
> pulling was very low, just about 0.3nm. My molecule name is QBH  and is out of
> membrane at bulk of the water and i want to pull it until center of bilayer.
> what must i do?

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