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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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