[gmx-users] pulling of ligand

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 13 12:47:20 CEST 2010

abdul wadood wrote:
> Dear GMX user
> I am working on enzyme ligand complex and want to calculate pmf of the 
> complex.
> I have successfully energy minimized and equilibrated the system.
> But when I pull the ligand from the complex using the md_pull.mdp file 
> then instead of ligand the protein is come out of the system.

Sounds like a normal consequence of periodic boundary conditions.  See FAQ #11:



> I have tried my best to solve the problem but not succeed.
> In the md_pull.mdp file I have given 1 for ligand and 0 for protein.
> If you kindly help me in this respect I will be very thankful to you.
> And your help will be highly appreciated.
> regards
> Abdul Wadood,
> Research Scholar,
> Dr.Panjwani Center for Molecular Medicine and
> Drug Research,
> International Center for Chemical and
> Biological Science,
> University of Karachi, Karachi-75720, Pakistan.
> Email:wadoodbiochemist at hotmail.com


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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