[gmx-users] Steered MD in gromacs

[Justin Lemkul]

On 9/3/13 11:22 AM, hanna pdb wrote:
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> Dear all,
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> 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

-- 
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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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