Yanmei Song wrote:
Yes, I want to get the equilibrium viscosity. My question is how I can
identify the system approach a zero acceleration after I try several
values. Thank you so much for your help.
Plot viscosity as a function of acceleration. Check the reference
(Wensink et al.) that I mailed earlier.
On Mon, Apr 20, 2009 at 10:17 AM, David van der Spoel
<sp...@xray.bmc.uu.se> wrote:
Yanmei Song wrote:
Dear David:
Thank you for your answer. i still have several questions.
Do I have to start the non-equilibrium simulation after the system
reach the equilibrium? Or I just need to start at the same starting
point as the my equilibrium systems?
At least equilibrium density.
What I need to do is just add the cos_acceleration: to the mdp file
and nothing else need to be changed, right? Also what do you mean by
"You need to do a few values such that you can extrapolate to zero
acceleration."
You are interested (I assume) in the equilibrium viscosity, therefore you
need to do this extrapolation. You can not assume that a small acceleration
is small enough.
After I finish the run, what option I should use for g_energy in order
to get the viscosity?
No option.
Just do it (tm).
Thank you so much in advance!
On Thu, Apr 16, 2009 at 11:33 PM, David van der Spoel
<sp...@xray.bmc.uu.se> wrote:
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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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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--
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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