[gmx-users] topology for oxygen molecule
mephysik at yahoo.com
Thu Apr 23 11:01:55 CEST 2009
For the study of diffusion of oxygen in water, I tried to search the itp file for oxygen molecule but could not find. Therefore, I have tried to make it myself.
Please tell me whether it is fine.
[ moleculetype ]
; molname nrexcl
OMOL 1 ; as there are two atoms in an oxygen molecule
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OB 1 OMOL OB1 0 0
2 OB 1 OMOL OB2 0 0
[ bonds ]
;ai aj funct c0 c1
1 2 1 1.244000000e-01 3.472866e+05; taken from Gaussian calculation.
[ pairtypes ] ; for non bonded interaction within each molecule with exclusion
; i j func c6 c12
OB OB 1 0.008261659 1.7392E-05;parameters from CRC Hand book of physics and chemistry.
;[ pairs ] no need of 1-4 interaction pairs as there are only two atoms.
; ai aj funct c6 c12
; 1 2 1 0.008261659 1.7392E-05;from CRC0
[ nonbond_params ]
; OB OW 1 0.004679059 6.853E-06; using L-B rule
; OB H 1 0 0; taken from OW-H
[ exclusions ]
1 2 ; because the nrexc1 is 1.
Please tell me where I am wrong.
for nonbonded interaction
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users