[gmx-users] Re: MD with RMSD restraint

[David van der Spoel]

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