[gmx-users] Re: g_vellac

Florian Dommert dommert at fias.uni-frankfurt.de
Fri Mar 6 12:56:13 CET 2009


On 06.03.2009, at 12:37, "Vitaly V. Chaban" <vvchaban at gmail.com> wrote:

> Hi,
> I checked the VACF calculation with the results obtained with my
> utility, it's completely correct with
> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
> where an.ndx contains all the number of atoms of the needed molecule.
sounds very good. In my opinion it is a question of units. After using  
g_analyze you end up with nm^2 / ps very uncommon for a diffusion  
coefficient. So if you convert this to more convenient units you  
should obtain the expected value.
> The problem is evidently in the integration. I suspect it's something
> with units there.
> Does
> g_analyze -integrate
> give a pure integral of the function supplied? '*1/3' is not performed
> (at least there is nothing about it in the manual)...
> Vitaly
>> Hi Flo,
>> Yes, I remember our talk about this problem about a year ago.
>> So what should be the correct notation now?
>> I just tried
>> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx
>> or
>> g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol
>> and then g_analyze -integrate -f vac.xvg
>> but they give me a value close to 0...

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