[gmx-users] Energy conservation in NVE simulations
Dear All, Below are more details on our efforts to maximize energy conservation in NVE runs with gromacs, while maintaining performance. I'd appreciate advice on the following: 1) Is this level of drift about "as good as it gets"? 2) Or, are there ways to make it even lower? 3) Are there settings we can dial back to improve speed without substantially increasing drift? Many thanks, Mike Gilson System: The system comprises 68679 waters, one protein with 6810 atoms, 8 sodium ions; total 75497 atoms The input file is below. We have deliberately turned off COM restraints because we are interested in how the protein moves. As noted before, for lincs-iter=4, the energy slope is approximately -0.01976 kJ/mol/ps; for lincs-iter=5, the slope is approximately 0.00991 kJ/mol/ps. Graphs of the energy for these respective conditions are provided here: https://drive.google.com/open?id=0B0zEqb9pykUWRHlqSEJTa2lwYkk https://drive.google.com/open?id=0B0zEqb9pykUWMWl0OEFtNGdVbzg MDP: ;DON'T POSITION RESTRAIN THE PROTEIN: NO -DPOSRES ;run parameters integrator = md ; leap-frog integrator nsteps = 1000 ; 0.001ps * 1000 = 10 ns dt= 0.001; 0.001ps smaller time step for NVE comm-mode= None ; let center of mass move, calculate diffusion constant ; Output control nstxout = 2 ; save coordinates every 0.5 ns nstvout = 2 ; save velocities every 0.5 ns nstenergy = 2 ; save energies every 0.5 ns nstlog = 2 ; update log file every 0.5 ns energygrps = protein non-protein ; Bond parameters continuation= yes ; starting after nvt.mdp constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds are constrained lincs_iter= 4 ; NVE requires high lincs-iter lincs_order = 4 ; accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; Frequency to update the neighbor list and long range forces rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) verlet-buffer-tolerance = 0.005 ; kJ/mol/ps per particle pbc = xyz ; periodic boundary conditions DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Pressure coupling is off pcoupl = no; fixed box size gives constant V ; Temperature coupling is off + no simluated annealing tcoupl = no ; NVE conditions ; Velocity generation gen_vel = no ; don't assign velocities: keep from thermalization -- 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.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 152, Issue 61
NIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 100 nstvout = 100 nstfout = 100 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 100 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency cutoff-scheme = Verlet nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.1 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb = 1.1 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 0.8 rvdw = 1.1 ; Apply long range dispersi0n corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 2 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 4e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 300 gen-seed = 173529 freezegrps = V freezedim = Y Y Y Thanks and Regards Sukriti [ https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D&X-OWA-CANARY=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.&retryCount=3 ] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: erian.ntu.edu.sg<http://www.ntu.edu.sg/home/xuzc/People.html> -- 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. -- -- Michael K. Gilson, M.D., Ph.D. Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences UC San Diego 9500 Gilman Drive La Jolla, CA 92093-0736 voice: 858-822-0622 http://gilson.ucsd.edu http://bindingdb.org http://drugdiscovery.ucsd.edu http://drugdesigndata.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.
