[gmx-users] Re: MD with RMSD restraint
sam.moors at chem.kuleuven.be
Tue May 19 09:25:44 CEST 2009
Position restraints do not allow me to do what I want.
For instance, I want to allow the system to freely explore the conformational
space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff.
Another application would be to push the system conformation away from the
reference structure, by using negative force constants.
Therefore the reference structure should be fitted to the simulation structure
(or the other way around) before calculating the position differences.
Thanks in advance for your help,
> 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.
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> End of gmx-users Digest, Vol 61, Issue 77
More information about the gromacs.org_gmx-users