[gmx-users] topology for oxygen molecule
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 23 13:58:41 CEST 2009
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
> ; 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
> Please tell me where I am wrong.
> for nonbonded interaction
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users