[gmx-users] Generation of the Distance Restraints

James Starlight jmsstarlight at gmail.com
Mon Mar 12 14:54:55 CET 2012

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,

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