[gmx-users] Re: g_vellac

Vitaly V. Chaban vvchaban at gmail.com
Fri Mar 6 13:11:00 CET 2009

It's like looking for a black cat in a dark room. If to multiply the
result by 1000 (derived from units) and divide it by 3 - the resulting
value seems to be close to the correct one.

Hope it's true. I will try to describe this tricky procedure in the
gromacs wiki now.


On Fri, Mar 6, 2009 at 12:56 PM, Florian Dommert
<dommert at fias.uni-frankfurt.de> wrote:
> 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...

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