[gmx-users] Generation of the Distance Restraints

[Mark Abraham]

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.

Mark