[gmx-users] Potential of mean force

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 20 14:28:59 CEST 2010

The tutorial to which you refer should give you all the necessary background to
apply pulling to a variety of systems.  In general, the procedure is the same.


Quoting abdul wadood <wadoodbiochemist at hotmail.com>:

> Dear gmx user
> First of all I am very thankful to all of you in helping me in the running of
> normal simulation using gromacs.
> Now, I want to calculate pmf for enzyme ligand complex. I search for correct
> direction but not found anywhere.
> There is tutorial on the gromacs website but it is for peptide peptide
> complex. Now, I dont understand how to specify the reference group to pull
> the ligand.
> The complex structure is attached.
> Any kind of help in this regard will be highly appreciated.
> Many 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
> _________________________________________________________________
> The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with
> Hotmail.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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