Hi, Admittedly, both the documentation on these features and the communication on the known issues with these aspects of GROMACS has been lacking.
Here's a brief summary/explanation: - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu which is essentially mdrun + OpenMM, hence it has some limitations, most notably it can only run on a single GPU. The performance, depending on setting, can be up to 10x higher than on the CPU. - GROMACS 4.6: the native GPU acceleration does supports only explicit solvent, mdrun + OpenMM is still available (exactly for implicit solvent runs), but has been moved to the "contrib" section which means that it is not fully supported. Moreover, OpenMM support - unless somebody volunteers for maintenance of the mdrun-OpenMM interface - will be dropped in the next release. I can't comment much on the implicit solvent code on the CPU side other than the fact that there have been issues which AFAIK limit the parallelization to a rather small number of cores, hence the achievable performance is also limited. I hope others can clarify this aspect. Cheers, -- Szilárd On Mon, Sep 23, 2013 at 7:34 PM, Francesco <frac...@myopera.com> wrote: > 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 -- 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
