Sunil Thapa wrote:
Respectable Justin/Mark
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
What about mass?
[ bonds ]
;ai aj funct c0 c1
1 2 1 1.244000000e-01 3.472866e+05; taken from Gaussian calculation.
You could also get this information from spectroscopic data, I believe. That
might make for an even more realistic model.
[ 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.
You don't need this. You are excluding nonbonded interactions between the two
OB atoms (nrexcl = 1), so there shouldn't be a pairwise interaction between them.
;[ 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.
Unnecessary. Again, you set nrexcl = 1, so this is taken care of.
Have you defined the appropriate [atomtype] somewhere, like the ff*nb.itp that
you're using?
-Justin
Please tell me where I am wrong.
for nonbonded interaction
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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