[gmx-users] Question for bdc = xy

[Mark Abraham]

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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