[gmx-users] PBC problem in bilayer system

[Tsjerk Wassenaar]

Hi,

Just a small side note. There's nothing intrinsically nonsensical about
translating more than a box size. The PBC are translation invariant, so you
can do anything and have the system be fine. However, for visualization,
translating one box length, and put the stuff back in the box, makes as
much sense as doing nothing at all.

Cheers,

Tsjerk
On Sep 14, 2014 3:55 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 9/14/14 9:52 AM, shahab shariati wrote:
>
>> Dear Justin
>>
>>
>> I did following:
>>
>>
>> trjconv -f *.xtc -s *.tpr -n *.ndx -o **.xtc -trans 6.46063 6.57889 9
>>
>> Based on your reply*, *I translated all system along the z.
>>
>> I used x and y according to box dimension.
>>
>> I used 9, instead of z dimension (8.30034), for z.
>>
>> When I see **.xtc using vmd, problem was not solved.
>>
>> Should I increase or decrease z value for -trans option?
>>
>>
> Start by following what I've told you:
>
> 1. Do not change x and y; set them to zero in -trans
> 2. A value of 9 for z makes no sense if your box is not that large; try 8
> or less
> 3. Use -pbc mol when translating
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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.
>