[gmx-users] Re: g_vellac

[Florian Dommert]

On 06.03.2009, at 13:11, "Vitaly V. Chaban" <vvchaban at gmail.com> 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
> <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...
>>>
>>
>