[gmx-users] Generation of the Distance Restraints

[Mark Abraham]

On 13/03/2012 1:13 AM, James Starlight wrote:
> Francesca,
>
> Yes I suppose this is good aproach for the generation of position 
> restricktions on the desired atoms. But I want to restrain the 
> distance between selected pairs of atoms ( e.g between C-alpha- 
> C-alpha atoms of two different residues).

The help for genrestr -disre says that this is exactly what it does... 
use an index group to make distance restraints.

>
> Also I want to restrain some dihedral angles in the desired rotameric 
> forms.
>
> In literature I've found that peple have dome the same things in 
> Gromacs but I could not find detailed algorithm of such methodology :(

There can't be a walk-through of everything anybody might ever do, 
unfortunately. Manual chapter 4 talks about the functional forms 
available. There's a table in section 5.5 that describes how to 
construct the line of a [ moleculetype ] section. That's all you need to 
know if have a general understanding of how the .top file works 
(elsewhere in chapter 5).

Mark

>
> James
>
> 12 ????? 2012 ?. 18:05 ???????????? francesca vitalini 
> <francesca.vitalini11 at gmail.com 
> <mailto:francesca.vitalini11 at gmail.com>> ???????:
>
>     I think you can make an index file using make_ndx where you specify
>     the atoms you want to restraint.
>     Hope this can help.
>     Francesca
>
>     2012/3/12 James Starlight <jmsstarlight at gmail.com
>     <mailto: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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