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.vitalin...@gmail.com
<mailto:francesca.vitalin...@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 <jmsstarli...@gmail.com
<mailto:jmsstarli...@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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