[gmx-users] oxygen gas parameters for simulation

vips g vipul_indian at rediffmail.com
Thu Apr 3 16:27:15 CEST 2008

Sir,    I am trying to simulate oxygen gas diffusion pathways in protein. 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 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 giving error that "force = inf on atom 1307". for oxygen 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      nrexcl  OXY               2[atoms]; nr    type    resnr residue   atom   cgnr   charge   mass#ifdef   _FF_OPLS  1    opls_968  
  1   OXY   OX1     1        0.00  2    opls_969   1   OXY   OX1      1       0.00#endifNow in the /top/  directory :- I added two atom types to file "ffoplsaa.itp" as  opls_968     15.99940  ; OX1  opls_969      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 in "ffoplsaabon.itp" OX1   OX2   1   0.12100 498000.0Now using the above parameters i m trying to simulate the system but getting errors as given above. Are these parameters  correct . Can someone provide me the parameters for oxygen gas so that my simulatio
 n can run.
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