[gmx-users] my minimization structure looks like a messy box?

Justin Lemkul jalemkul at vt.edu
Wed Dec 13 18:27:01 CET 2017

On 12/13/17 12:24 PM, Shi Li wrote:
>> ------------------------------
>> Message: 6
>> Date: Wed, 13 Dec 2017 11:41:26 -0500
>> From: MD <refmac5 at gmail.com>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] my minimization structure looks like a messy
>> 	box?
>> Message-ID:
>> 	<CAPPXTgRhhwOV-+nEbc2m4_NjSJcmWHo37hmFFz3TbqE7PAkHAw at mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>> It looks like this
>> https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD
>> On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> If you are talking about all the lines, try using “-pbc mol" in the trjconv, this should get rid of all of them. But I haven’t have that after em.mdp. Did you generate velocity in energy minimization?

There can be no velocities during energy minimization. The snapshot 
provided just suggests a solute that was not centered in the box prior 
to carrying out EM, hence it is "broken" across boundaries.



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

303 Engel Hall
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