[gmx-users] Protein goes out of the box

[spss4 at iacs.res.in]

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

----- End message from Justin Lemkul <jalemkul at vt.edu> -----