Hi, I am not an expert in non-EQ MD, but a simulation time of 1ns for a collective property in a honey-like substance like an IL sounds very short. However, from my colleagues in the group of Prof. Müller-Plathe, who applied non-EQ MD to derive viscosities, I heard that this method is quite reliable. Take a look at their papers. As far as I can remember, the first authors of the papers were Whei Zhao or Simon Butler.
/Flo > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Boning Wu > Sent: Tuesday, July 09, 2013 3:00 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] Calculating shear viscosity using none-equilibrium MD: > Viscosity dependent on acceleration magnitude > > Hi GMX Users, > I want to calculate the shear viscosity of an ionic liquid. Thus I > applied the cos-acceleration in my box. However, I found that my calculated > viscosity got by "g_energy" is significantly dependent on magnitude of the > acceleration. I don't know why. Even if this is a none-Newton liquid,why > viscosity cannot converge at such a slow acceleration My system consists > of 216 ion pairs, and it has been equibrated under NPT for 5 ns. The box > length is about 5 nm. > > ******* > Magnitude of the acceleration(nm/ps2) Viscosity(cP) > 0.01 6102 > 0.03 4452 > 0.06 3580 > 0.1 872 > 0.5 48.5 > Experimental Value 85 > ******* > Here is my mdp file > > ************************************** > title = XXXX YYYY > cpp = /lib/cpp > define = > integrator = md > dt = 0.001 > nsteps = 1000000 > nstxout = 50000 > nstvout = 50000 > nstlog = 50000 > nstenergy = 100 > nstxtcout = 5000 > xtc-grps = XXXX YYYY > nstlist = 10 > ns-type = grid > rlist = 1.5 > coulombtype = PME > rcoulomb = 1.5 > rvdw = 1.5 > tcoupl = Berendsen > tc-grps = XXXX YYYY > tau-t = 0.1 0.1 > ref-t = 298 298 > Pcoupl = NO > ref-p = 1.0 > gen-vel = yes > gen-temp = 298 > gen-seed = 173529 > constraints = none > cos-acceleration = 0.5 > *************************************** > Thank you advance for your help! > Boning > > -- > Boning Wu > Graduate student > Department of Chemistry and Chemical Biology > Rutgers, the State University of New Jersey > Piscataway, NJ, 08854 > boning...@rutgers.edu > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
