Re: [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 
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  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

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

==
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Re: [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 
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  wrote:
>
> > Hi gromacs users,
> >
> > How to do potential energy surface scan for organic molecule using
> Gromacs?
> >
> > What are the steps?
> >
> > Thanks,
> > Neha
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
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Re: [gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Mark Abraham]

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  wrote:

> Hi gromacs users,
>
> How to do potential energy surface scan for organic molecule using Gromacs?
>
> What are the steps?
>
> Thanks,
> Neha
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] POTENTIAL ENERGY SURFACE SCAN

[Neha Gupta]

Hi gromacs users,

How to do potential energy surface scan for organic molecule using Gromacs?

What are the steps?

Thanks,
Neha
-- 
Gromacs Users mailing list

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