VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Sun Feb 10 2013 - 03:01:41 CST

Dear Jeff

Thank you very much for your reply,

Exactly, 1.54 A, this is my bond distance, But I do not know how I can
solve it,

How Can I solve it to include my intermolecular contribution,please?

On Sun, Feb 10, 2013 at 4:40 AM, Jeffrey Potoff <jpotoffx_at_gmail.com> wrote:

> On 02/09/2013 09:29 AM, Ali Alizadeh wrote:
>
>> Dear All users
>>
>> I am simulating the decane molecules(C10H22, NPT Ensemble, 420 K and 1
>> bar, 60 chain, Lammps). My parameters is related to a paper,
>>
>> When I represent g(r), I get exotic values:
>>
>> 1- My peaks have high values( more than 5000!, for ch2-ch2) and
>>
>
> That's because your g(r) includes intramolecular contributions. Your
> large first peak is probably around 1.54 A, which happens to be the bond
> length between carbon atoms in alkanes.
>
> Regards,
> Jeff
>
> --
> ==============================**==============================**==========
> Jeffrey J. Potoff jpotoff_at_wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ==============================**==============================**==========
>
> 

-- 
Sincerely
Ali Alizadeh