[gmx-users] cgnr

[David van der Spoel]

Marcelo A. Carignano wrote:
> 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?

Could be, please submit a bugzilla.

> 
> 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
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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