[gmx-users] translate problem

[gromacs query]

Hi Justin,

>> If that doesn't work, trjconv can translate

Thanks a lot, trjconv works fine. For some reason I could not achieve this
with editconf.

regards,
JIom

On Mon, Mar 2, 2015 at 1:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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