[gmx-users] gromacs bond restraints

[Neha Gandhi]

Hi Mark,

I came across your tutorial on REMD on gromacs website. In the tutorial,
you don't mention about dihedral or any other restraints during REMD. Sorry
for my ignorance, but I am trying to figure out if restraints are required
for residues such as prolines to stop going to cis during REMD above 350K
or there is any setting which will be take care of it?

Many thanks,
Neha






On 16 January 2014 14:59, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> See chapter four for what is available, and tables in 5.5 for a summary of
> their use.
>
> Mark
> On Jan 16, 2014 5:11 AM, "Neha Gandhi" <n.gandhiau at gmail.com> wrote:
>
> > How can I impose restraints in gromacs .mdp file or topology file to
> > avoid isomerization of the peptide bond at the highest temperatures?
> >
> > Your help is appreciated
> >
> > --
> > Regards,
> > Dr. Neha S. Gandhi,
> > Curtin Research Fellow,
> > School of Biomedical Sciences,
> > Curtin University,
> > Perth GPO U1987
> > Australia
> > LinkedIn
> > Research Gate
> > --
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-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate