Quoting Mark Abraham <[EMAIL PROTECTED]>: > > 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.
Using unconstrained_start = yes seems to have alleviated my problems. My NVT simulation ran nicely, and my NPT is currently going well. Thank you very much! -Justin Justin A. Lemkul Department of Biochemistry Virginia Tech _______________________________________________ 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
