[gmx-users] RE: Targeted MD

Ran Friedman r.friedman at bioc.uzh.ch
Fri Aug 20 17:17:46 CEST 2010


-r and -rb are for FEP.

If you want to bias your simulation's sampling, you can use the pull
code, essential dynamics sampling or flooding, all of which are
described in the manual and literature.


Nimesh Jain wrote:
> Hello,
> I realize that this topic has been discussed before, but I just need
> to ascertain a few things: I have a system of about 1400 atoms with
> implicit solvent and I want to do a targeted MD. While doing the
> pre-processing, if I just specify "grompp -r in.gro -rb out.gro", is
> this sufficient or are there any other things that I need to consider.
> Also, I have tabulated potentials.
> If any one knows how to do this, or if you need more info on my
> system, please let me know.
> Thanks,
> Nimesh

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