[gmx-users] Re: g_msd and pbc

[Dr. Vitaly V. Chaban]

>
> Thanks Tsjerk for the information. It would be very nice if you can
> elaborate it. I am unable to understand.
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Thu, Dec 8, 2011 at 12:10 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
>> Hi Chandan,
>>
>> Pretty simple; you just take the smallest distance between the time
>> points in the periodic system.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury <iitdckc at gmail.com>
>> wrote:
>> >
>> > Dear gmx_users,
>> >
>> > I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the
>> > PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer
>> > and at some point of the trajectory, some lipid molecules, due to PBC in
>> the
>> > lateral direction, might pop out from one side of the box and re-ener
>> from
>> > the other side. I such a situation it should show a very lage msd, but
>> > actually in the g_msd code, this fact is taken care of. Can some one
>> > explain, how is this effect taken care of.
>> >

In periodic system, there is infinite number of images of each
particle. You should always consider the smallest possible distance
[between the image of the two particles].


-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA