[gmx-users] Fwd: Question about editconf -noc flag

[Justin Lemkul]

On 7/29/15 2:32 AM, James Lord wrote:
> Hi all,
> I have made an oil slab (energy minimized, equilibrated nvt and npt), some
> of the oil molecules are at the other end (periodicity).
> https://drive.google.com/open?id=0B0YMTXH1gmQsYmdvQ3huYWtDaGs
>
> then I decided to increase the box size in z direction a bit to make enough
> room for protein, using
>
> editconf -f OCT_npt.gro -oOCT_newbox.gro -box  6.47271 6.47271 16 -noc
>
> https://drive.google.com/open?id=0B0YMTXH1gmQsT1M3dzBNNTJrT28
>
> I used the last flag to put the oil at the ends of box but it is not doing
> for one end? any thoughts?

You have broken molecules.  Make them whole with trjconv before resizing the 
box.  Note that with -noc, your slab will always be on one "end" of the box, but 
the distinction between "ends" is irrelevant with periodicity.

-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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