Also, why in vacuo? At least turn on an implicit solvent model.
Gianluca
On Tue, 3 Sep 2013, Justin Lemkul wrote:
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
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