Fw: [gmx-users] Umbrella Sampling _ pulled ion

Justin Lemkul jalemkul at vt.edu
Fri Jul 26 18:19:44 CEST 2013

Please remember to keep the discussion on the list.

On 7/26/13 12:04 PM, Shima Arasteh wrote:
> what I aim to see is that the pulled ion should be remained in center of the channel (peptide inserted in lipid bilayer).
> I didn't restrain the channel, it makes a little bit hard for me to judge exactly. Is position restraint of channels essential here?

The data in pullx.xvg indicate that the distance between the reference group and 
the pulled group was maintained at -1.2 nm.  Visual inspection of the trajectory 
will tell you whether or not that is the position you desire.  Having noted the 
output of grompp (you did that, right?) you can match up the input 
specifications and target restrained distance and the actual outcome.

Unless something has gone completely haywire, the outcome is very predictable. 
Learning to assess the validity of what you have done through careful 
record-keeping and cross-referencing with input files will prevent you from 
having to wait around for people on the Internet to check your work ;)



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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