[gmx-users] Generation of the Distance Restraints

francesca vitalini francesca.vitalini11 at gmail.com
Mon Mar 12 15:05:11 CET 2012

I think you can make an index file using make_ndx where you specify
the atoms you want to restraint.
Hope this can help.

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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