[gmx-users] Generation of the Distance Restraints
Mark.Abraham at anu.edu.au
Mon Mar 12 15:42:33 CET 2012
On 13/03/2012 12:54 AM, James Starlight wrote:
> 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
... which should read "-n index.ndx". Please get in the habit of copying
and pasting actual command lines that you have observed to function like
you think they do :-). Then you won't mis-type something sometime that
will cause everyone to waste their time.
> 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 ?
You need an index file that has a group or groups that do what you want.
Some details on the webpage. Since you know already the 2 atoms you care
about, you can make it in a text editor faster than writing this email
:-) Or indeed just constructing a [ distance_restraints ] section of the
[ moleculetype ] in consultation with the information in chapters 4 and
5 faster still.
> 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)?
Only by choosing a gentle restraint at first and picking a time interval
at which to increase it.
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