[gmx-users] Visualization of conf.gro and confout.gro

[Justin Lemkul]

On 1/7/16 2:04 PM, Chang Woon Jang wrote:
> Dear Gromacs Users,
>
>     I did NPT simulations with a system containing 15000 atoms of polymers.
>
> Initially, conf.gro was visualized in VMD and showed all connections are
> OK. However, the confout.gro (final output configuration) seems to look
> bad. Some of bonds are disconnected at the outer surface which I guess the
> boundary of simulation box. I think that this is due to the periodic
> boundary conditions.
>
> The question is,
>
> If I use the correct topology files, does the confout.gro file can be used
> for the further simulation no matter how the visualization look like?
>

Of course.  The topology is definitive in terms of connectivity and 
interactions.  You can use trjconv to "fix" the coordinates for the purposes of 
visualization, but mdrun doesn't care because it doesn't affect the physics.

-Justin

-- 
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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

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