> Hi guys, I have a question regarding the run time for energy minimization, > nvt and npt equilibration steps. Currently, I am doing a RNA-protein > simulation (using ff amber14 and spce water model) in a 10 A octahedron box > containing almost 400k solute atoms. > For the energy minimization step, I did it for 2 ns and received a
>There is no time in EM, only number of steps. I used 1,000,000 steps for EM (I have always assumed 1,000,000 step to be 2ns) > potential E of nearly -2.25e-7. >Check your exponent :) Surely your system does not have an energy of (effectively) zero. You are correct. Hahahaha. I didnt even the error. My potential E is actually -2.25e-7. Is that a good number? > I am also doing 2ns for nvt and npt equilibration steps. > My question is: is 2ns too long for these steps? >You need to run long enough for the observable(s) of interest to converge. Have they? The observable of interest? Do you mean temperature and density by it? I am still running it and it has been runing over 4 days (nvt run) on my mbp. > Also another question regarding running simulation on a cluster: do I need > to install gromacs mpi to run it on parallel? Is it necessary since I read > in the literature gromacs would use all the available cores to run if I > dont specify the number of cores. >Depends on the configuration of the cluster, how many cores you intend to use, >etc. Everything is here: >http://www.gromacs.org/Documentation/Acceleration_and_parallelization >Consult with your sysadmin for best performance on whatever hardware you have. I will talk to my sysadmin about it. Thanks, Thanh Le -- 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.