VMD-L Mailing List

From: Rameswar Bhattacharjee (rameswariacs_at_gmail.com)
Date: Thu Jun 11 2020 - 00:35:06 CDT

Thank you very much Axel for your explanation. It will be very helpful to
interpret the data. As there are very few water molecules the bulk density
of water is low so the normalization factor is also smaller. I got your
point. Thank you

On Thu, Jun 11, 2020 at 12:59 AM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> On Thu, Jun 11, 2020 at 12:26 AM Rameswar Bhattacharjee <
> rameswariacs_at_gmail.com> wrote:
>
>> Hi all,
>> I have a simulated periodic box of pentanol with very few amounts of
>> water. I have plotted the g(r) for OW-OW for the system using vmd and I got
>> the first peak at a very high value of g(r) (~80). It looks very odd to me.
>> Is there a normalization issue (bulk density) as I have few water
>> molecules?
>>
>
> whether you get correct normalization depends on whether you feed the g(r)
> plugin correct data, e.g. with the correct boundary box.
>
> if you have very few water molecules, then the peaks *must* have larger
> absolute values than for a (pure) bulk system.
> please think about what it is that you are computing!
> g(r) is the ratio of the probability of finding an OW atom at distance r
> in your system relative to that of an ideal gas.
> the fewer OW atoms you have the smaller the normalization factor is that
> you have to divide by. now what happens, if you divide the same number by a
> large number versus a small number?
>
>
>> I am using lammps for the simulation. Any suggestion will be highly
>> appreciated. Thank you.
>>
>
> there is not enough information to give an authoritative answer. one can
> only speculate.
> however, the measure gofr command in VMD has been thoroughly tested over
> many years (and several bugs found and fixed (some of them quite subtle)),
> it gives consistent results with other well testing implementations and is
> used by many people. that makes it now very unlikely that there are any
> significant bugs remaining. it is much more likely that either your
> interpretation of the data is not correct or your computation was not
> correctly done.
>
> axel.
>
>
>
>>
>> --
>> *Regards*
>> *Rameswar*
>>
>> *********************************************************************
>> *Dr. Rameswar Bhattacharjee*
>> University of Delaware
>> *Newark, DE-19716*
>> *********************************************************************
>>
>>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
*Regards*
*Rameswar*
*********************************************************************
*Dr. Rameswar Bhattacharjee*
Postdoctoral Researcher
University of Delaware
*Newark, DE-19716*
*********************************************************************