[gmx-users] (no subject)

[Justin Lemkul]

On 4/23/18 5:08 PM, rose rahmani wrote:
> Hi,
>
> I have a capped amino acid in box of water and ion(but the system is not
> charged) and named it initial.gro, i can see some unreal bonds when i open
> it with VMD(H atom has 2 bonds!). And when i open it with gaussview C and H
> atom where nonbobded and were single atoms around remained bonded
> structure.( maybe aminoacid in initial.gro file didn't get well optimized
> or anything... )
>
> But when i run nvt, the amino acid structure get real structure and
> everything is ok.
>
> I remember Justin said that MD and GROMACS can't make or break bond. So
> What happend to my system?

You had lousy initial coordinates, which showed up as a badly distorted 
geometry. It should look normal after energy minimization (which it 
probably did, otherwise NVT equilibration never would have worked).

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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