Dear gmx-users I am experiencing some problems running a protein-protein docked structures in water(GROMOS43a1/SPC)with gmx-4.0.4 using 8 CPUs.
I have 20 docked (protein-protein) structures of one common protein with two different homologous protein, 10 from each group and started simulations for all, using same parameters. I did energy minimization for all the systems, all systems reached to energy minimized configuration in between 10000 to 12000 steps using steep algorithm and PE for all minimized systems are vary between -3975853 to -3571906 KJ/mol. In final MD out off 10 simulations 9 from each group was crassed in between 200 ps to 900 ps with lincs warning. However one simulation from each group running well up to 5 ns, and after 5ns out of these two, one simulation crassed with too many lincs warning, while other one completed 20ns and steel continue. when restarting the *crashed *simulation feeding "-cpi md.cpt" to mdrun the simulation restarts fine with few steps before but stopped at same portion of the simulation with same lincs warning. I checked the energy and temperature distribution and find that potential energy is fine,however total energy of systems as well as temperature (300K attain 321K at last steps) is higher at last steps before simulation stops.I read all the mailing least before posting this question but did not reach any conclusion. Any explanation or solution for this, why one simulation is stable and running fine up to more than 20ns however others are crassed with same parameters?? I am thinking that it may be because of steric class between docked protein. Is it mean that one docked structure making more natural interaction in compare to other docked structures??? Regards Sanjay Kumar Upadhyay Research Scholor Protein Dynamics lab Dept of Chemistry IIT Powai, Mumbai, 400076 Ph no. 09920200345, 09699353562, -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
