[gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Neha Gupta]

Thank you for the reply.

I am given to understand that, we are supposed to run em.mdp and md.mdp
file for the organic molecule of interest.

After that, we are supposed to run

mdrun -s md.tpr -rerun configuration.pdb

What are the factors should we take care of while running md.mdp?

How do we mention the dihedral angle of our interest?

Could you please elucidate?


Thanks,
Neha







On Fri, Jun 16, 2017 at 2:39 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Generate your configurations with some other tool, put them in a trajectory
> file, and use
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
> Mark
>
> On Fri, 16 Jun 2017 11:13 Neha Gupta <nehaphysics17 at gmail.com> wrote:
>
> > Hi gromacs users,
> >
> > How to do potential energy surface scan for organic molecule using
> Gromacs?
> >
> > What are the steps?
> >
> > Thanks,
> > Neha
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