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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
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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________________________________________________________________________
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