Yanmei Song wrote:
Hi, David:
I performed the NEMD and got the following results for averaging the
last 1 ns. So the second column should be the acceleration and last
column should be the 1/viscosity. But notice that there are so many
big negative numbers, which makes the average negative. Can you help
me out here? what would be possible reason for this.
xmgrace will tell you which is which, I think the first is shear
viscosity and the second bulk viscosity. Your system might be too smal
(Berk Hess recommends at least 1000 molecules) or the simulation too
short. However bulk viscosity is much more difficult to get right.
Once more, read the literature, and use the tools (xmgrace) the
information is in the xvg file, but you cut it out here.
1000.000061 -0.007012 -369.713501
1020.000061 0.006066 320.372314
1040.000000 0.002330 122.940369
1060.000000 -0.001427 -75.253372
1080.000000 0.002888 152.323944
1100.000000 0.005696 300.385651
1120.000000 0.002224 117.322388
1140.000000 0.005990 316.127655
1160.000000 0.008966 472.723846
1180.000000 0.004485 236.538010
1200.000000 -0.000249 -13.136140
1220.000000 0.005020 264.962219
1240.000000 0.009248 488.308197
1260.000000 -0.000559 -29.509850
1280.000000 -0.003190 -168.296112
1300.000122 0.002394 126.418747
1320.000122 0.003682 194.374222
1340.000122 0.000371 19.600368
1360.000122 -0.002311 -122.002975
1380.000122 0.001776 93.685326
1400.000122 -0.003357 -177.067062
1420.000122 -0.002963 -156.359772
1440.000122 -0.001078 -56.895496
1460.000122 -0.002273 -119.947853
1480.000122 -0.000658 -34.716648
1500.000122 -0.000928 -48.969398
1520.000122 0.003464 182.804337
1540.000122 -0.001149 -60.652023
1560.000122 0.004629 244.299088
1580.000122 0.000485 25.557356
1600.000122 0.002339 123.374527
1620.000122 0.002612 137.982239
1640.000122 0.002827 149.150589
1660.000122 -0.001614 -85.147079
1680.000122 0.005144 271.660522
1700.000122 -0.002053 -108.302643
1720.000122 0.006096 321.414948
1740.000122 0.006021 317.682129
1760.000122 -0.001203 -63.409481
1780.000122 0.000394 20.755482
1800.000122 0.001910 100.748962
1820.000122 -0.001588 -83.742523
1840.000122 0.002268 119.578842
1860.000122 0.002422 127.769302
1880.000122 -0.000288 -15.188296
1900.000122 0.003324 175.257568
1920.000122 0.003688 194.440231
1940.000122 0.005800 305.705505
On Mon, Apr 20, 2009 at 11:31 AM, David van der Spoel
<sp...@xray.bmc.uu.se> wrote:
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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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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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.
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