On 06.03.2009, at 13:11, "Vitaly V. Chaban" <[email protected]> wrote:
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.
Perfect, isn't it ?
Hope it's true. I will try to describe this tricky procedure in the
gromacs wiki now.
So I have no concern and thanks for putting this into the wiki.
Flo
Vitaly
On Fri, Mar 6, 2009 at 12:56 PM, Florian Dommert
<[email protected]> wrote:
Hi,
On 06.03.2009, at 12:37, "Vitaly V. Chaban" <[email protected]>
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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