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 <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 >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-us...@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-requ...@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. >>> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >>> _______________________________________________ >>> gmx-users mailing list gmx-us...@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-requ...@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. > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-us...@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Department of Chemical Engineering ASU _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
