[gmx-users] rdf

[nishap.patel at utoronto.ca]

Hi Will,

     I have been using pme from the very start and it didn't help with  
the volume. Could you please elaborate on what you mean by average  
g(r) over every molecule?

    And because my rdf-s are not smooth enough even with 100ns, I get  
fluctuating data using rdf-s.

-Nisha




Quoting Will Glover <will_glover at yahoo.com>:

> Hi,
> 100 ns is overkill for those liquids.  It should be smooth enough at  
>  1 ns, provided you average g(r) over every molecule.
> What do you mean the volume decreases?  With time?
>
> As for the cut-off, it's well known that switching Coulomb terms   
> leads to artifacts, and increasing the cut-off distance doesn't   
> necessarily make things converge.  See   
> http://pubs.acs.org/doi/abs/10.1021/ct0502256 for example.
>
> Use PME for electrostatics.
>
> Regards,
> --
> Will
>
> --- On Sat, 1/30/10, nishap.patel at utoronto.ca   
> <nishap.patel at utoronto.ca> wrote:
>
>> From: nishap.patel at utoronto.ca <nishap.patel at utoronto.ca>
>> Subject: [gmx-users] rdf
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Date: Saturday, January 30, 2010, 9:45 PM
>> Hi,
>>
>>   I am doing rdf's of simple molecules. I ran my
>> simulation of water and methane for 100ns to get a smoother
>> curve for the rdf. I am trying to determine the volume, and
>> after a certain cut-off I would assume my values to be
>> constant (i.e. volume), but the values fluctuate alot (i.e.
>> decreasing). If I am using 'switch', from say 0.8-0.9,
>> shouldn't the values smooth off after 0.9nm? and stay
>> constant after that? Any insights would be helpful.
>>
>> Thanks.
>>
>> Nisha P
>>
>>
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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536