[gmx-users] Question for bdc = xy
jalemkul at vt.edu
Fri Mar 21 21:52:36 CET 2014
On 3/21/14, 4:43 PM, ookami a wrote:
> I just checked previous posts, they said increasing the size of z-direction
> to create a vaccum layer would be working.
> So I extend my z-direction with 3 times of the original box, when I run the
> pvt process, the vacuum layer disappeared.
As you should expect. If you apply pressure to no resistance, it shrinks.
> How could I modified my nvt.mdp file? From the pre posts, seems they don't
> have any problem when running the nvt.
Indeed, because the box is fixed. If you want commentary on your .mdp file,
you'll need to post it and explain fully what the system is. Anything else is
just blind guesswork, which is not productive for anyone.
> Thank you very much.
> On Fri, Mar 21, 2014 at 8:24 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 3/20/14, 11:51 PM, ookami a wrote:
>>> Dear all:
>>> I'm trying to set up a bdc only with xy, so I edited my mdp file with
>>> changing the bdc =xyz to bdc = xy.
>>> However, I got a error message which is "Can not have Ewald with pbc=xy"
>>> Anyone know how to solve it?
>> Per the manual, you can't use an Ewald summation method or pressure
>> coupling in this case, unless you are using walls.
>> 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
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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
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