[gmx-users] Question for bdc = xy

[ookami a]

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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/
>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>