[gmx-users] energy minimization problem

[Justin Lemkul]

On 6/1/15 8:06 AM, soumadwip ghosh wrote:
> Thanks Justin for your quick reply. What are the correct non-bonding
> settings for CHARMM to be used in the .mdp file?
>

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

I seem to have to post this information weekly...

> Here is how the CNT molecule looks like prior to energy minimization.
>
> pre energy min CNT
> <https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing>
>

Yep, that's definitely wrong.

> I am not continuing any of the equilibration steps anymore. As you can see
> the CNT structure is distorted badly.
>
> Please help me out. What settings do I need to change in order to avoid
> such distortion? Is there a possibility that the cnt topology was wrong to
> begin with?
>

The CNT topology is clearly wrong.  It's probably missing some bonds or something.

-Justin

-- 
==================================================

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

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