[gmx-users] Pulling

Justin Lemkul jalemkul at vt.edu
Sat Dec 27 15:46:40 CET 2014

On 12/25/14 2:49 PM, asasa qsqs wrote:
> 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?

In principle, that should work, but you haven't said how long you conduct the 
pulling or shown what the distance time series is doing.  Is QBH approaching the 
DMPC membrane over time, or just staying at some distance?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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