[gmx-users] Generation of the Distance Restraints

[francesca vitalini]

Well I'm kind of new to the problem too and I'm actually doing
something similar. For the dihedral restraints you have to add to your
topology a specific section specifying the atoms you want to
restraint. For the distance restraints use genrestr with the option
-disre and the appropriate index file (you can specify the atom of the
residue you want when creating the index file through make_ndx).
Check this out
http://www.gromacs.org/Documentation/How-tos/Distance_Restraints
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints?highlight=Position+Restraints
Francesca

2012/3/12 James Starlight <jmsstarlight at gmail.com>:
> Francesca,
>
> Yes I suppose this is good aproach for the generation of position
> restricktions on the desired atoms. But I want to restrain the distance
> between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two
> different residues).
>
> Also I want to restrain some dihedral angles in the desired rotameric forms.
>
> In literature I've found that peple have dome the same things in Gromacs but
> I could not find detailed algorithm of such methodology :(
>
> James
>
> 12 марта 2012 г. 18:05 пользователь francesca vitalini
> <francesca.vitalini11 at gmail.com> написал:
>>
>> I think you can make an index file using make_ndx where you specify
>> the atoms you want to restraint.
>> Hope this can help.
>> Francesca
>>
>> 2012/3/12 James Starlight <jmsstarlight at gmail.com>:
>> > Dear Gromacs users!
>> >
>> >
>> > I want to perform constrained MD simulation of my protein with inclusion
>> > of
>> > some experimental restraints.
>> >
>> >
>> > 1) I found that genrest cpmmand could be usefull for the generation of
>> > the
>> > distance restrictions wich I could use in my constrined simulation.
>> >
>> > Also in manual I've found that command like
>> >
>> > genrestr -f b2ar.gro -disre -index.ndx -o test.itp
>> >
>> > will produce some distance restricted matrix of the whole groups
>> > presented
>> > in the index.ndx file.
>> >
>> > So how I could select to contrain selected residues within selected
>> > distance
>> > by means the index file?  E.g I've manually point out 2 residues in
>> > index.ndx. I waant to preserve between that residues some desired
>> > distance D
>> > wich I've obtaine from the experimental data. How I could do it via
>> > genrestr
>> > and waht addition flags should I use for that purpose ?
>> >
>> >
>> > 2) Is there any way to apply gradually the desired dist.resrs during
>> > MDrun
>> > to prevent some artifacts in my system wich would occur due to the rapid
>> > application of the dis.res ( e.g in cases where the conformation of the
>> > started structure and that wich I'd obtained fter application of the
>> > restrains are slightly different)?
>> >
>> > Thanks for help,
>> >
>> >
>> > James
>> >
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>>
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