Thanks for being so clear Mark. Best, Albert
On 05/11/2015 03:18 PM, Mark Abraham wrote:
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.
-- --------------------------------- 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.
