[gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Justin Lemkul]

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.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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-- 
==================================================

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
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================