[gmx-users] Problem with dihedral restraints

[gangotri dey]

Thank you for the kind reply. I will compute and update in the post.



*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254




On Fri, Aug 4, 2017 at 10:31 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You should expect changes, you're not freezing the angles in place. You're
> making it less energetically favourable for them to change. But if the
> environment is strong enough, they'll respond to that. Increase kfac by a
> factor of a thousand and they'll probably not move noticeably. Whether that
> is a good idea is something you might find out later :-)
>
> Mark
>
> On Fri, Aug 4, 2017 at 4:16 PM gangotri dey <holyriver6 at gmail.com> wrote:
>
> > Hello!
> >
> > I posted a question a few days back and I got a reply but it still does
> not
> > work.
> >
> > I have a small drug molecule that I would like to compute. I want to
> > restraint the Ramachandran dihedral angles. I have used the following
> lines
> > in the .itp file for the molecule. It was suggested that I increase the
> > force constant, which I did. However, I still see the change in the
> > dihedral angles after the NVT, NPT and Production run. I am not sure how
> > best it can be implemented.
> >
> >
> >
> > [ dihedral_restraints ]
> > ; ai   aj    ak    al  type  phi  dphi  kfac
> > 698 702 692 691 1 -142.56 0 100
> > 719 712 716 698 1 -84.24 0 100
> >
> > 702    698    716    712     1    50.3766     0 100
> > 695    691    692    702     1  -166.8294     0 100
> >
> >
> > My .mdp file is similar to the one used in the Bevan lab tutorial online.
> >
> >
> >
> >
> > *Thank you*
> >
> > *Gangotri Dey*
> > --
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