[gmx-users] Re: MD with RMSD restraint

[David van der Spoel]

Sam Moors wrote:
> 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) ?
> 
If the averaging is purely harmonic there is no difference. For this, 
turn off r^-3 averaging etc. in the mdp file.


> 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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> 
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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