[gmx-users] MD with RMSD restraint

David van der Spoel spoel at xray.bmc.uu.se
Sat May 16 10:46:41 CEST 2009

Mark Abraham wrote:
> Sam Moors wrote:
>> Hi gmx users/developers,
>> I would like to do a molecular dynamics simulation with a restraint on 
>> the backbone RMS deviation from a reference structure.
>> Does anybody know if this is possible?

How about position restraints only on the backbone? Same effect.

> Not exactly as you describe, but you should read the section in chapter 
> 4 of the manual and see for yourself.
>> If yes, could you explain how to do it?
>> If no, what would be the easiest way to implement this in gromacs?
> It could be done, but I'm not sure it's worth the effort.
> Mark
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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