Hi, Stuff was probably broken here before 4.6. I would trust only single threaded in 4.6 and later, and only after comparing with 4.5.
Mark On Mon, 11 May 2015 14:50 Albert Solernou <a.soler...@leeds.ac.uk> wrote: > Hi All, > I am thinking of running an implicit solvent simulation using Gromacs > (.mdp file pasted at the end of the email). However, I am a bit > concerned about its accuracy as I get different results for the > Polarisation term. More specifically, the first step of an energy > minimisation gives different values for this energy term depending on > the number of threads/processes that I use (while the rest of the E. > terms are exactly the same). I tried the Intel compilers + MKL, and the > GNU compilers + ACML, as well as GMX versions 5.0.4 and 5.1-beta1. I > could even get a segfault with the GNU compilers and ACML when using 2 > "processes" (gmx mdrun -nt 2). > > The question is simple. Am I doing anything wrong? Is there any > precaution that I should take? > > Cheers, > Albert > > ----------------------------------------------- > ; minim.mdp - used as input into grompp to generate em.tpr > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.01 ; Energy step size > nsteps = 50000 ; Maximum number of (minimization) steps > to perform > > ; Parameters describing how to find the neighbors of each atom and how > to calculate the interactions > nstlist = 1 ; Frequency to update the neighbor > list and long range forces > cutoff-scheme = Group > ns_type = grid ; Method to determine neighbor list > (simple, grid) > coulombtype = Cut-Off ; Treatment of long range > electrostatic interactions > rcoulomb = 999.0 ; Calculate all long range interactions > rvdw = 1.2 ; Short-range Van der Waals cut-off > pbc = no ; Periodic Boundary Conditions (yes/no) > > ; Implicit solvent parameters: > implicit-solvent = GBSA ; use implicit solvent > gb-algorithm = OBC ; use the OBC approach for the GB > radius > gb-obc-alpha = 1 ; parameters correspond to OBC-II > gb-obc-beta = 0.8 ; > gb-obc-gamma = 4.85 ; > gb-epsilon-solvent = 78.5 ; as seen in the original paper. > sa-algorithm = Ace-approximation ; include surface area > contribution for non-polar atoms > sa-surface-tension = 0.0054 ; default value. > > -- > --------------------------------- > Dr Albert Solernou > EPSRC Research Fellow, > Department of Physics and Astronomy, > University of Leeds > Tel: +44 (0)1133 431451 > > -- > 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.