[gmx-users] Protein goes out of the box

[Justin Lemkul]

On 4/26/17 1:13 AM, spss4 at iacs.res.in wrote:
>  ----- Message from Justin Lemkul <jalemkul at vt.edu> ---------
>     Date: Tue, 25 Apr 2017 10:40:40 -0400
>     From: Justin Lemkul <jalemkul at vt.edu>
> Reply-To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Protein goes out of the box
>       To: gmx-users at gromacs.org
>
>> On 4/25/17 10:35 AM, spss4 at iacs.res.in wrote:
>>> Hii all,
>>> I have simulated protein in 45% ethanol water mixture for 100ns. After
>>> completion of the job I saw that maximum portion of my protein goes out
>>> of
>>> the box. Then I have done trjconv -pbc mol to the trajectory file. After
>>> trjconv some portion of the protein is still out of the box. I want to
>>> see
>>> the local environment of the protein using the .gro file(last frame) but
>>> some portion of protein is dry. How can I get the actual state of
> protein
>>> after completion of 100ns?
>>
>> You may need a few iterations of trjconv to get what you want.
>>
>>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
>> 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
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-request at gromacs.org.
>> Hii Justin
>
> Thank you so much for your reply.I am a new user of gromacs. Should I use
> -pbc mol -center for my case? Is this give me the actual state of protein

I stand by the contents of the link I posted before.  A simple protein in 
solution should be trivial to recenter, but you'll have to figure out what works 
based on that linked information.

> after 100ns? Please correct me if I am wrong.

That's the structure your simulation predicts for that time point, but a single 
snapshot is not nearly as useful as the ensemble the simulation produces.

-Justin

-- 
==================================================

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

==================================================