[gmx-users] Re: g_velacc

David van der Spoel spoel at xray.bmc.uu.se
Sun Aug 31 09:18:31 CEST 2008

Florian Dommert wrote:
> Hello,
>  regard the topic about calculating diffusion coefficients, I also have 
> a question regarding the code of g_velacc.
> To calcalute the diffusion coefficient of a molecule with the help of 
> its VACF, I think the center of mass velocity the protein is required. 
> However there is no possibility to extract the VACF of molecule directly 
> from a trajectory because g_velacc does not calulate VACFs of molecules, 
> only Momentum ACFs. To finally obtain the VACF of molecule you have to 
> divide the MACF of a molecule through the square of the mass of the 
> molecule.
> Is there a special reason, why it is not possible to get the VACF for a 
> molecule straightforward from g_velacc ?
No special reason, just mundane ones: computing the diffusion constant 
through mean square displacement is easier in terms of convergence. At 
leat this was the case 12 years ago when these tools were written. If 
you feel like creating a patch which does this automatically then this 
would be appreciated.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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