[gmx-users] Re: Is openmp necessary?

[Hsin-Lin Chiang]

Hi Mark,

Thank you for your reply.
I understand now.

Sincerely yours,
Hsin-Lin
>>> 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
>