[gmx-users] pbc problem

[Mark Abraham]

To make this clear, center the trajectory on the water and watch the time
evolution in some visualization program.

Mark


On Sun, Oct 27, 2013 at 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/27/13 12:05 PM, shahab shariati wrote:
>
>> Dear Tsjerk Wassenaar
>>
>> Very very thanks for your reply.
>>
>> I used trjconv -pbc mol.
>>
>> pbc problem was solved only for lipid molecules.
>>
>> When I see new trajectory by vmd, there are some problesm about drug
>> molecule.
>>
>> https://www.dropbox.com/s/**xq4s6az17buhvb8/images-2.docx<https://www.dropbox.com/s/xq4s6az17buhvb8/images-2.docx>
>>
>> If I show my system as 4 regions, my system before equilibration is as
>> fallows:
>>
>> region (1): water + drug
>> region (2): top leaflet of bilayer
>> region (3): bottom leaflet of bilayer
>> region (4): water
>>
>> After equilibration, drug molecule exits region (1) and enters region (4),
>> alternately.
>>
>> On the other hand, drug molecule is in region (1)in some frames and is
>> in region (4) in other frames.
>>
>> Please tell me how to fix it? Is this issue (about drug molecule) pbc
>> problem?
>>
>>
> As has already been stated several times, there is no problem at all.  The
> outcome is completely normal, and there are not discrete regions (1) and
> (4). It is a continuous block of water via PBC.  The molecule can freely
> diffuse throughout it.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
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>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==============================**====================
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