[gmx-users] diffusion coefficient

[David van der Spoel]

On 2011-12-09 08:34, Mark Abraham wrote:
> On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:
>> I want to calculate the diffusion coefficient of a small polypeptide
>> with g_msd (see here
>> http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant)
>>
>> because of periodic boundary condition, when the peptide goes out of
>> the right side it comes in from left side, which leads to an
>> artificial displacement. this will give rise to a non-realistic MSD.
>>
>> is g_msd intelligent enough to avoid this artificial displacement?
>>
>
Yes it is.

> Not sure about g_msd, but you can take care of it yourself with a
> workflow derived from the information here
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
> Mark


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se