[gmx-users] oxygen gas parameters for simulation
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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