[gmx-users] Re: MD with RMSD restraint

[Massimiliano Bonomi]

Another possibility is to patch gromacs with PLUMED

http://merlino.mi.infn.it/~plumed/PLUMED/Home.html

Here  RMSD  (and derivatives) is already implemented and you can
easily restraint your MD simulation within a certain RMSD cutoff
from a reference structure.

Massimiliano

On May 19, 2009, at 9:31 AM, David van der Spoel wrote:

> 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
> _______________________________________________
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