[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Mon Apr 23 23:37:31 CEST 2018

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 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


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