[gmx-users] Re: g_velacc

[Dr. Vitaly Chaban]

"g_integrate" should be "g_analyze" below. Sorry.



On Fri, Jul 5, 2013 at 12:20 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> 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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>
>