[gmx-users] fixing PBC view

[Netaly Khazanov]

Thanks a lot for your help! Indeed it works for me.

On Sun, Feb 7, 2016 at 9:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/7/16 7:48 AM, Netaly Khazanov wrote:
>
>> Hi All,
>> My system is including the small compound with penetrates the membrane
>> lipids. I've ran the MD simulation and now trying to get rid off the PBC
>> view and create a nice movie. The problem that I've managed to fix PBC
>> view
>> of the lipids, however the location of small compound still indicates the
>> wrong position related to membrane. Any ideas how to fix it will be
>> appreciated.
>> The command that I used:
>>   trjconv_d -s md.tpr -f md.xtc -o md_noPBC.pdb -pbc mol -center -n -ur
>> compact # centering on POPC group
>> I've used the numerous variation  but none does work.
>>
>>
> Most likely you need to fit the small molecule's position with, e.g. -fit
> transxy after the above centering command.
>
> -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 visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Netaly