[gmx-users] cgnr

[Marcelo A. Carignano]

Cutoff I set at 3.00 nm
The distance between the two molecules is about 0.1 nm.
The box is a cube of 20 nm 

A bug perhaps?

Marcelo.

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of David van der Spoel
Sent: Thursday, May 04, 2006 3:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cgnr

Marcelo A. Carignano wrote:
> Thank you David, but there is no such a term in this case:
> 

I see, make the cut-off larger. mdrun uses charge group based cutoff 
(see chap 4) and you are probably missing some interactions in the 
second case.

> 
> $g_energy
> ....
> (deleted lines)
> ....
> 
> 
>   Select the terms you want from the following list
> -----------------------------------------------------
> LJ-(SR)        Coulomb-(SR)   Potential      Kinetic-En.    Total-Energy

> Temperature    Pressure-(bar) Vir-XX         Vir-XY         Vir-XZ

> Vir-YX         Vir-YY         Vir-YZ         Vir-ZX         Vir-ZY

> Vir-ZZ         Pres-XX-(bar)  Pres-XY-(bar)  Pres-XZ-(bar)  Pres-YX-(bar)

> Pres-YY-(bar)  Pres-YZ-(bar)  Pres-ZX-(bar)  Pres-ZY-(bar)  Pres-ZZ-(bar)

> #Surf*SurfTen  Mu-X           Mu-Y           Mu-Z           T-rest

> 
> 
> Any other suggestion?
> 
> 	Thank you,
>                     Marcelo.
> 
> 
> Marcelo A. Carignano wrote:
>> Dear all:
>>
>> I'm running a test case defining all the interaction parameters in the
>> topol.top file. My system consist of two NH3 molecules.
>> Every thing goes well except for the role played by the "cgnr" values:
>> Depending on how I assign these numbers the calculated Coulombic
>> interaction changes. If I put the four atoms in the same group, the
>> energy is not correct. If I put the four atoms in four different chnr's,
>> the Coulombic interactions are OK:
>>
> 
> David wrote:
> 
> 
> check the 14 energy.
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
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