# [gmx-users] Non-equilibrium Viscosity Calculation

Yanmei Song ysong30 at asu.edu
Tue Apr 21 07:51:56 CEST 2009

```Hi, David;

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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 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
>>>>>>>>
>>>>>>> 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!
>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>> interface
>>>>>>> or send it to gmx-users-request at gromacs.org.
>>>>>>> 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
>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/search before
>>>>> posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>> interface
>>>>> or send it to gmx-users-request at gromacs.org.
>>>>> 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
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-users-request at gromacs.org.
>>> 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
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>

--
Yanmei Song
Department of Chemical Engineering
ASU

```