On 8/8/13 3:57 PM, rookie417 wrote:
Dear GROMACS users,
I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulations later
during analysis. The simulations ran normally and the PMF plots look
accurate. However, I realized that position restraints were not applied only
after looking at the log files and position restraints energy values were
missing. The umbrella sampling MD simulation was for 2 ns only and I checked
the pullx-umbrella.xvg files and the COM fluctuations are not that bad
considering its only a short time for convergence.
Can anyone comment on how not using position restraints would effect the
result otherwise?
Position restraints are generally not necessary. Please refer to our paper that
is associated with the umbrella sampling tutorial to understand why we used them
in this particular case.
-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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