[gmx-users] Re: MD with RMSD restraint

[Sam Moors]

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.

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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>
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> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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