On 6/16/17 6:16 AM, Neha Gupta wrote:
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?
You need to generate a series of conformations as a function of the changing
dihedral. It's a bit tedious to do in GROMACS, but essentially, you apply
[dihedral_restraints] to the configuration and then energy-minimize the
structure. Then, using a topology *without* restraints, simply calculate the
single-point energy of the minimized structure. Follow the link Mark provided
closely.
-Justin
Thanks,
Neha
On Fri, Jun 16, 2017 at 2:39 PM, Mark Abraham <mark.j.abra...@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 <nehaphysic...@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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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
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