Good afternoon everybody, I'm a bit confuse about gromacs performances with implicit solvent.
I'm simulating a 1000 residues protein with explicit solvent, using both a cpu and a gpu cluster. With a gpu node (12 cores and 3 M2090 gpu ) I reach 10 ns/day, while with no gpu and 144 cores I got 34 ns/day. Because I have several mutants (more than 50) I have to reduce the average simulation time and I was considering different option such as the use of implicit solvent. I tried with both the clusters and using gromacs 4.6 and 4.5 but the performances are terrible (1 day for 100ps) comparing to the explicit solvent. I read all the other messages on the mailing-list and the documentation, but the mix of old and new "features"/posts really confuses me a lot. Here (http://www.gromacs.org/Documentation/Acceleration_and_parallelization) it is said that with the gpu 4.5 and implicit solvent I should expect a "substantial speedup". Here ( http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM#Benchmark_results.3a_GROMACS_CPU_vs_GPU ) I found this sentence "It is ultimately up to you as a user to decide what simulations setups to use, but we would like to emphasize the simply amazing implicit solvent performance provided by GPUs." I follow the advise found in the mailing list and read both the documentation (site and manual), but I can't figured it out what should I do. How can you guys have amazing performances? I also found this answer from a last March post (http://gromacs.5086.x6.nabble.com/Implicit-solvent-MD-is-not-fast-and-not-accurate-td5006659.html#none) that confuses me even more. "Performance issues are known. There are plans to implement the implicit solvent code for GPU and perhaps allow for better parallelization, but I don't know what the status of all that is. As it stands (and as I have said before on this list and to the developers privately), the implicit code is largely unproductive because the performance is terrible. " Should I skip the idea of using implicit solvent and try something else? these are a set of parameters that I used (also the -pd flag) ; Run parameters integrator = sd tinit = 0 nsteps = 50000 dt = 0.002 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout = 5000 xtc_precision = 1000 energygrps = system ; Bond parameters continuation = no constraints = all-bonds constraint_algorithm = lincs lincs_iter = 1 lincs_order = 4 lincs_warnangle = 30 ; Neighborsearching ns_type = simple nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 ; Electrostatics coulombtype = cut-off pbc = no comm_mode = Angular implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii = 0 gb_epsilon_solvent = 80 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 0.0054 ; Temperature coupling tcoupl = v-rescale tc_grps = System tau_t = 0.1 ref_t = 310 ; Velocity generation gen_vel = yes ld_seed = -1 thank you for the help. cheers Francesco -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- 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