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

2017-12-17 Thread Dilip H N 
Hello,
You need to use -pbc mol in your command for viewing the trajectory, then
this issue will be solved.



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On Wed, Dec 13, 2017 at 11:23 PM, MD  wrote:

> ah, that explains. thanks Justin!
> Ming
>
> On Wed, Dec 13, 2017 at 11:42 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/13/17 11:41 AM, MD wrote:
> >
> >> It looks like this
> >> https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD
> >>
> >
> > That's classic PBC.
> >
> > -Justin
> >
> >
> > On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul  wrote:
> >>
> >>
> >>> 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
> >>>
> >>> jalem...@vt.edu | (540) 231-3129
> >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>>
> >>> ==
> >>>
> >>> --
> >>> Gromacs Users mailing list
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> >>>
> >>>
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] my minimization structure looks like a messy box?

2017-12-13 Thread MD 
ah, that explains. thanks Justin!
Ming

On Wed, Dec 13, 2017 at 11:42 AM, Justin Lemkul  wrote:

>
>
> On 12/13/17 11:41 AM, MD wrote:
>
>> It looks like this
>> https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD
>>
>
> That's classic PBC.
>
> -Justin
>
>
> On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul  wrote:
>>
>>
>>> 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
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] my minimization structure looks like a messy box?

2017-12-13 Thread 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 <refm...@gmail.com>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] my minimization structure looks like a messy
        box?
Message-ID:
<cappxtgrhhwov-+nebc2m4_njsjcmwho37hmffz3tbqe7pak...@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 <jalem...@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

--
==

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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

2017-12-13 Thread Shi Li 

> 
> --
> 
> Message: 6
> Date: Wed, 13 Dec 2017 11:41:26 -0500
> From: MD <refm...@gmail.com>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] my minimization structure looks like a messy
>   box?
> Message-ID:
>   <cappxtgrhhwov-+nebc2m4_njsjcmwho37hmffz3tbqe7pak...@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 <jalem...@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
>> 
>> jalem...@vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>> 
>> ==
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>> 
> 
> 
> --
> 
> Message: 7
> Date: Wed, 13 Dec 2017 11:42:46 -0500
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Hydrophobic and hydrophilic SASA for a
>   particular portion of a protein
> Message-ID: <7db09a5f-e531-fc2f-a190-b07776b07...@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
> 
> jalem...@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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Re: [gmx-users] my minimization structure looks like a messy box?

2017-12-13 Thread Justin Lemkul 



On 12/13/17 11:41 AM, MD wrote:

It looks like this
https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD


That's classic PBC.

-Justin


On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul  wrote:



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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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--
==

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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

2017-12-13 Thread MD 
It looks like this
https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD

On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul  wrote:

>
>
> 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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] my minimization structure looks like a messy box?

2017-12-13 Thread Justin Lemkul 



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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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

2017-12-13 Thread MD 
Hi Gromacs folks,
Any of you have experienced having a messy box looking gro file after
em.mdp?
Ming
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