[gmx-users] Re: MD with RMSD restraint

[Sam Moors]

Hi David,

Thanks for your suggestion.
However, I have a problem with the use of distance restraints in gromacs. As 
described in the manual a restraint potential is applied to each pair of atoms
separately. Instead, I would like the restraint potential to depend on the
root mean square of pair distance deviations, i.e. distance-based RMSD as you
suggest.
Maybe I can use the "averaging over multiple pairs" facility, If I change the
averaging function (power 2 instead of 6) ?

Thanks again,
Sam

>
> 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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