[gmx-users] Question for bdc = xy

[ookami a]

I want my system to be simulated in only two dimension periodic boundary
condition. but for this one, after the pvt, everything spread in the whole
box(where z_direction is 3 times the original length of the box) and the
vacuum disappeared. so i think this system is still simulated with xyz
dimension.


On Thu, Mar 27, 2014 at 5:48 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> You'll have to post your image to a file sharing service, not this list.
>
> Why do you think your result is unphysical?
>
> Mark
>
>
> On Thu, Mar 27, 2014 at 8:16 PM, ookami a <mengxz2 at vt.edu> wrote:
>
> > I think I describe it wrong.
> > After nvt process, my box size doesn't change but, there is no separate
> > vacuum layer, all the molecules are spread through the whole box.
> >
> > Just as the image shown. Do you know why does this happen?
> > Thank you very much!
> >
> >
> > On Thu, Mar 27, 2014 at 2:09 PM, ookami a <mengxz2 at vt.edu> wrote:
> >
> > > I think I describe it wrong.
> > > After nvt process, my box size doesn't change but, there is no separate
> > > vacuum layer, all the molecules are spread through the whole box.
> > >
> > > Just as the image shown. Do you know why does this happen?
> > > Thank you very much!
> > >
> > >
> > >
> > > On Fri, Mar 21, 2014 at 4:50 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >
> > >>
> > >>
> > >> On 3/21/14, 4:43 PM, ookami a wrote:
> > >>
> > >>> Hi,
> > >>> 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.
> > >>
> > >> -Justin
> > >>
> > >>
> > >>  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
> > >>>>
> > >>>> --
> > >>>> ==================================================
> > >>>>
> > >>>> 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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> > >>>>
> > >> --
> > >> ==================================================
> > >>
> > >> 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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> >
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