[gmx-users] GROMACS viscosity questions

[Chris O'Brien]

Dear gmx-users:

I would like to investigate the viscosity of polylactide with GROMACS.  I 
have made (nearly) all of the necessary changes to the parameter files, but 
I am curious about the workings and capabilities of gromacs.  My amorphous 
systems have about 72,000 atoms, and my crystalline systems (pbc = full) 
have 14,400.  Can viscosity phenomena be examined in realistic time frames 
on systems of these sizes?

Does anybody know if equilibrium or non-equilibrium methods would be more 
appropriate for these systems?  Will I need fully equilibrated (NPT) states 
to start viscosity simulations?  If this is feasible, would it be possible 
for somebody to post sample .mdp files that you used for your viscosity 
simulations?

Is there any additional documentation available about the fluctuation 
option (-fluc) for g_energy and the viscosity outputs?  Is this a reliable 
method to obtain viscosity information (either from runs designed to 
extract viscosity information or from other runs)?

Thank you,
Chris O'Brien

Department of Chemical Engineering
Clemson University
Clemson, SC  29634-0909
USA