[gmx-users] Re: g_velacc

Dr. Vitaly Chaban vvchaban at gmail.com
Fri Jul 5 12:20:34 CEST 2013

Use this command line:

-- g_velacc -nonormalize -acflen 2001
-- g_integrate -f vac.xvg -integrate
-- Multiply the resulting value by 333.333, the result will be
self-diffusion coefficient expressed as result * 10^(-9) m^2/s.

The velocities should be written down at least every 10fs during MD. The
required trajectory depends on system viscosity. The higher it is, the
longer trajectory (and larger acflen) is necessary for relevant results.

Dr. Vitaly V. Chaban

On Fri, Jul 5, 2013 at 11:10 AM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2013-07-05 10:50, Ishwor wrote:
>> I have taken the fit for 2ns in Einsteins curve to calculate the diffusion
>> coefficient but when i take the values up to 100 ps for velocity auto
>> correlation i get the matching result...Is it good to do such thing? i
>> will
>> be happy if you guide me.
>> I have attached the graph of VAC herewith.
>> Thanks <http://gromacs.5086.x6.**nabble.com/file/n5009582/vac.**jpeg<http://gromacs.5086.x6.nabble.com/file/n5009582/vac.jpeg>
>> >
>> --
>> View this message in context: http://gromacs.5086.x6.nabble.**
>> com/g-velacc-**tp5009541p5009582.html<http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009582.html>
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>  The graph does not show the tradition ripples. If this is for water the
> result could be ok with 100 ps, but you still need to have decent sampling
> (e.g. 20 fs) of the velocities since they change rapidly.
> --
> 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
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