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

[Justin Lemkul]

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

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

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