[gmx-users] topology for oxygen molecule

[Justin A. Lemkul]

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
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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
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

========================================