[gmx-users] pbc problem
mark.j.abraham at gmail.com
Sun Oct 27 18:11:48 CET 2013
To make this clear, center the trajectory on the water and watch the time
evolution in some visualization program.
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
>> If I show my system as 4 regions, my system before equilibration is as
>> 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),
>> 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
> 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 A. Lemkul, Ph.D.
> 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 <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
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