On 9/3/13 11:22 AM, hanna pdb wrote:
Dear all,
I am just starting MD simulations and wanted to see how to perform steered molecular dynamics in
gromacs . Most papers and tutorials that I found were done in NAMD. Can anyone recommend examples
that were done in gromacs? In my case the tutorial " Pull Code and Umbrella Sampling" on
the gromacs website seems not applicable. I "simply" want to see how to perform an in
vacuo simulation by pulling.
Indeed, my tutorial will go beyond what you want, but I don't see how it's not
applicable. There is discussion of how to use all (or at least most) of the
pull settings and produce a SMD trajectory as part of the protocol.
-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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