For example, a 3ns simulation using a tau_p of 0.5 I get a surface tension of 30 dynes/cm and using a tau_p of 5.0 I get a surface tension of 25 dynes/cm.
First thing that comes to mind is that your area per lipid is not at equilibrium. Assuming that your bilayer normal lies in the Z dimension, plot your xy area vs. simulation time. My bet is that it is not converged and that the run using a tau_p of 0.5 is approaching convergence faster than the run using a tau_p of 5.0. Once it is converged, I would recommend something more like 20ns for a production run.
Is this difference negligible?
Test that out yourself. Do some repeats, or perhaps take the 3ns snapshot from the simulation at tau_p of 0.5 and continue it using a tau_p of 5.0. Also take the 3ns snapshot from the simulation at tau_p of 5.0 and continue it using a tau_p of 0.5.
Therefore, is it more reliable when simulating a lipid bilayer system to use a short tau_p ~0.5ps or a longer tau_p ~ 5.0ps?
Sorry, I don't know the answer to that one. Chris. _______________________________________________ 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
