I am trying to perform a simulation of 128 dppc in 3655 spc water. I obtained .pdb and .top files from the Biocomputing website at U.Calgary. I do nothing to alter the structure, which must be minimized as it comes from the end of a 1 ns simulation. Processing the input files works fine, but the mdrun always ends somewhere between step 500 and step 3000. I have tried adjusting various parameters, such at the time step, tau_p, tau_t and the compressibility, but nothing has created a consistent run. I wonder where I should be focusing my time to solve this problem. Should I focus on the parameters and structure, or computer hardware/software?
Thanks for any suggestions --Mike Skaug University of California Davis _______________________________________________ gmx-users mailing list [email protected] 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
