[gmx-users] PBC problem in bilayer system

[Justin Lemkul]

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

-- 
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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

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