[gmx-users] Non-equilibrium Viscosity Calculation
Yanmei Song
ysong30 at asu.edu
Tue Apr 21 07:51:56 CEST 2009
Hi, David;
Thank you so much for your prompt response. Your answer is really helpful.
On Mon, Apr 20, 2009 at 10:31 PM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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
>>>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>>>> posting!
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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
>>>>> posting!
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>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>>
>>>>
>>>
>>> --
>>> 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 posting!
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>
--
Yanmei Song
Department of Chemical Engineering
ASU
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