[gmx-users] translate problem

[Justin Lemkul]

On 3/2/15 6:46 AM, gromacs query wrote:
> Hi All,
>
> I have membrane thickness along Z and want to merge peptide in membrane. I
> need to translate peptide (say 10 Angs) along -Z to adjust its position and
> used command like this:
>
> editconf -f pep.pdb -c -princ -rotate 0 90 0 -translate -10 0 0 -o
> new_pep.pdb
>
> It seems that it does not move at all. But when I used '-translate -100000
> 0 0' then it moved a little along -Z. I am not sure whats wrong. Please
> suggest. Also in VMD the center of pep does not pass through the principal
> axis (slightly off center).
>

First, GROMACS uses nm as its unit for all distances, not A, so to translate 10 
A, you need -1 along z.  Also, using -translate without specifying a box, IIRC, 
causes a simple translation of everything, e.g. no net movement within the unit 
cell.  Try adding an explicit -box definition.  If that doesn't work, trjconv 
can translate, but you need a -pbc option to do a relative translation within 
the box rather than just translating everything.

-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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