[gmx-users] Non-equilibrium Viscosity Calculation

Yanmei Song ysong30 at asu.edu
Tue Apr 21 01:01:54 CEST 2009 

  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.

  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
<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
>>> _______________________________________________
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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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> or send it to gmx-users-request at gromacs.org.
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>



-- 
Yanmei Song
Department of Chemical Engineering
ASU

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