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

[Shi Li]

> 
> ------------------------------
> 
> 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?

Shi
>> 
>> 
>> On 12/13/17 11:02 AM, MD wrote:
>> 
>>> Hi Gromacs folks,
>>> Any of you have experienced having a messy box looking gro file after
>>> em.mdp?
>>> 
>> 
>> Probably http://www.gromacs.org/Documentation/Terminology/Periodic_
>> Boundary_Conditions but you'll have to define "messy" if that's not
>> what's going on.
>> 
>> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
>> 
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> 
> ------------------------------
> 
> Message: 7
> Date: Wed, 13 Dec 2017 11:42:46 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Hydrophobic and hydrophilic SASA for a
> 	particular portion of a protein
> Message-ID: <7db09a5f-e531-fc2f-a190-b07776b07f8c at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> 
> 
> On 12/13/17 11:22 AM, Sudip Das wrote:
>> Dear All,
>> 
>> Is there any tool available that can calculate hydrophobic and hydrophilic
>> (solvent accessible) surface areas *for a particular portion (not the
>> whole)* of a protein?
> 
> Yes, you can get that from gmx sasa. Generate a surface for the whole 
> protein, and choose whatever subset of that surface that you want as the 
> output.
> 
> -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.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
> ==================================================
> 
> 
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> End of gromacs.org_gmx-users Digest, Vol 164, Issue 39
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