> Hello all, > > I'm having a few more problems running an NVT ensemble on my system. I > have an > integral membrane protein, with a transmembrane helix and small > extracellular > domain. The bilayer is DPPC. I have one face of the bilayer solvated to > surround the extracellular domain in water, and there are 3 sodium > counterions. > I have successfully energy-minimized this system to a reasonable > potential > energy (as mentioned previously on the list). I want to run short NVT and > NPT > equilibration steps before running full-out MD simulations. I'm having > some > trouble getting it started. I have attached my nvt.mdp file below, along > with > an excerpt from my md.log file that highlights the problem. Is there > something > obvious I'm missing? No matter what I try, the temperature and pressure > at Step > 0 are always something extremely high.
Have you done the minimization with the constraints enabled? Whether or not this is true, you probably want to use unconstrained_start = yes, since the constraint algorithms are routinely applied after the integration step. For equilibration with RF, I tend to use tau_t as low as 0.01, but I do not think this is your problem. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
