Quoting vips g <[EMAIL PROTECTED]>: > 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
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. -Justin 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 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. ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
