[gmx-users] Pulling code

asasa qsqs sanaz_dr_m at yahoo.com
Wed Dec 24 23:49:16 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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