[gmx-users] Re: g_vellac

[Florian Dommert]

Hi,


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.
Cheers
Flo
> 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...
>