Hi, There are some known issues fixed in 4.6 ( http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x) but since the authors of this code haven't added any test cases, AFAIK it could have gotten broken at any time. I can't see any obvious .mdp issues. I would encourage you to attempt to replicate the original work, and see what that tells you.
Mark On Fri, Dec 18, 2015 at 3:33 AM Mateusz Jasik <mateusz.ja...@pwr.edu.pl> wrote: > Dear Gromacs Users, > > I am trying to obtain the shear viscosity of an imidazolium-based ionic > liquid by using periodic perturbation method. While recalculating some of > mine old data, it turned out, that the results I get from the Gromacs 4.6.7 > are different from those obtained from Gromacs 4.5.5 by two orders of > magnitude. > > As a test I have run a calculations using the same tpr files (created by > the 4.5.5 verison) and two versions of gromacs. The mdp file I used is > presented below: > > title = nvT MD > integrator = md > constraints = all-bonds > dt = 0.001 > nsteps = 12000000 > nstenergy = 100 > nstlist = 10 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 100 > nstxtcout = 1000 > xtcprecision = 1000 > ns_type = grid > coulombtype = PME > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.0 > tcoupl = nose-hoover > tc_grps = MENIM Tf2N > tau_t = 0.1 0.1 > ref_t = 303.15 303.15 > Pcoupl = No > gen_vel = no > gen_temp = 298 > gen_seed = 173529 > energygrps = MENIM Tf2N > constraint_algorithm = LINCS > pbc = xyz > cos_acceleration = 0.01 ; I have run simulations for five > different values, ranging from 0.01 to 0.05 > > > I obtained the 1/Viscosity values using "g_energy -f edr_file -s tpr_file > -o output.xvg". > > Here are the values I got from the program: > > cos_acceleration 1/Viscosity (4.5.5) 1/Viscosity (4.6.7) > 0.01 0.0583586 > 5,91038 > 0.02 0.3713 > 57,4981 > 0.03 1.24583 > 211.699 > 0.04 2.73402 > 475.518 > 0.05 4.02399 > 807.279 > > There have previously been numerous threads regarding the viscosity > calculations, but I haven't found any with the problem similar to this. Are > there any differences between the two version of program that can influence > this value? And if so, which one should I treat as the more reliable? Or > could this be a problem from my side (for example with the parameters used)? > > Thanks and regards, > Mateusz > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.