[gmx-users] Re: MD with RMSD restraint

[Marc Baaden]

Hi,

Sorry to pull a self-publicity plug, but you could use our MDDriver 
library [1] to implement whatever constraint you want as long as it 
can be calculated from the system positions and translates into
forces to be applied to your system.
Such a 'scripting' application is very briefly hinted at in the
corresponding paper [2].

Cheers,
Marc

[1] http://www.baaden.ibpc.fr/projects/mddriver/
[2] http://dx.doi.org/10.1002/jcc.21235

>>> David van der Spoel said:
 >> Sam Moors wrote:
 >> > Hi,
 >> > 
 >> > 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.
 >> 
 >> Then you have to derive a force that is the derivative of the RMSD with 
 >> respect to the positions. This may be difficult, since you have the 
 >> superposition step in between.  What you could do straight away is move 
 >> from normal RMSD to distance-based RMSD, in which case the this has been 
 >> implemented using distance restraints. You would use genrestr to 
 >> generate the additional topology input, then determine a suitable force 
 >> constant and Bob's your uncle.
 >> 
 >> Cheers.
 >> > 
 >> > Thanks in advance for your help,
 >> > Sam
 >> > 
 >> >>
 >> >> 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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 >> 
 >> -- 
 >> 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
 >> http://www.gromacs.org/mailman/listinfo/gmx-users
 >> 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
 >> 

Marc Baaden

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217