[gmx-users] oxygen gas parameters for simulation

Thu Apr 3 16:27:15 CEST 2008

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 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; OXY&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&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.
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