[gmx-users] Non-equilibrium Viscosity Calculation
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 21 07:31:45 CEST 2009
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
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> On Mon, Apr 20, 2009 at 11:31 AM, David van der Spoel
> <spoel at 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
>>> <spoel at 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
>>>>> <spoel at 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.
>>>>>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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.
>>>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
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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.
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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