Yanmei Song wrote:
Dear All:
I wanted to get the viscosity of my simulated polymer system. From the
manual it said that : GROMACS also has a non-equilibrium method for
determining the viscosity" (page 123) Does this mean I just need to do
a separate non-equilibrium MD run? In terms of mdp file, I just need
to add the following options, right?
acc_grps:
accelerate:
cos_acceleration:
Just the last one.
My question is: first, how to set the value of cos_acceleration: ?
You need to do a few values such that you can extrapolate to zero
acceleration.
Second, after I finish the run, how can I get the viscosity from the
simulation result? Anyone has done this yet? Thank you so much for
your answer in advance.
g_energy.
J Chem Phys 116 (2002) 209-217
J Chem Phys 119 (2003) 7308-7317
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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