[gmx-users] Generation of the Distance Restraints
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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