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 <sp...@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 >> <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 >>> >> >> >> > > > -- > 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