[gmx-users] oxygen gas parameters for simulation

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 3 16:46:10 CEST 2008

Quoting vips g <vipul_indian at rediffmail.com>:

> Sir, &nbsp;&nbsp; I am trying to simulate oxygen gas diffusion pathways in
> protein.&nbsp;For this I am usinf OPLS force fields. I have used a cubic box
> of 0.8 in which the protein is centered. Now I added 200&nbsp;oxygen gas
> molecule along with spc water molecule using genbox which runs successfully.
> Now When I start the simulation it crashes at the first step&nbsp;giving
> error&nbsp;that "force&nbsp;= inf on atom 1307".&nbsp;for

So what is that atom?  What is near it?  Likely in creating your system, you
generated some severe atomic overlap between components of your system. 
There's no way for us to know, so you'll have to look into that one.


PS - Using plain-text formatting is your friend, especially for those of us who
have text-based mail clients :-)  Don't know if anyone else had a hard time
reading this mail, but I definitely did.

> oxygen&nbsp;molecule i am using a pdb which contains two oxygen atomtypes OX1
> and OX2 which I have generated from chem sketch.I have also made an
> "oxygen.itp" file like "spc.itp" file.[molecule type ];
> molname&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; nrexcl&nbsp;
> 2[atoms]; nr&nbsp;&nbsp;&nbsp; type&nbsp;&nbsp;&nbsp; resnr
> residue&nbsp;&nbsp; atom&nbsp;&nbsp; cgnr&nbsp;&nbsp; charge&nbsp;&nbsp;
> mass#ifdef&nbsp;&nbsp; _FF_OPLS&nbsp;
> 1&nbsp;&nbsp;&nbsp;&nbsp;opls_968&nbsp;&nbsp;
>   1&nbsp;&nbsp; OXY&nbsp;&nbsp; OX1&nbsp;&nbsp;&nbsp;&nbsp;
> 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.00&nbsp; 2&nbsp;&nbsp;&nbsp;
> opls_969&nbsp;&nbsp;&nbsp;1&nbsp;&nbsp; OXY&nbsp;&nbsp;
> OX1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
> 0.00#endifNow in the /top/&nbsp;&nbsp;directory :- I added two atom types to
> file "ffoplsaa.itp" as&nbsp; opls_968&nbsp;&nbsp;&nbsp;&nbsp; 15.99940&nbsp;
> ; OX1&nbsp; opls_969&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15.99940 ; OX2- I added
> opls_968 and opls_969 atom types with parameters same as that for opls_002
> atom type with charge 0.000 in file "ffoplsaanb.itp"- I added bond length and
> bond energy for oxygen
> gas&nbsp;in&nbsp;"ffoplsaabon.itp"&nbsp;OX1&nbsp;&nbsp; OX2&nbsp;&nbsp;
> 1&nbsp;&nbsp; 0.12100 498000.0Now using the above parameters i m trying to
> simulate the system&nbsp;but getting errors as given above.&nbsp;Are these
> parameters&nbsp; correct . Can someone provide me the parameters for oxygen
> gas so that my simulatio
>  n can run.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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