Re: [gmx-users] Energy Conservation with 4fs timestep
rlist 1.3 did the trick, thanks. Why did I not see this problem with PME-switch? Thanks, Ilya 2009/4/1 Berk Hess > > > > Date: Wed, 1 Apr 2009 14:15:05 +1100 > > From: mark.abra...@anu.edu.au > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] Energy Conservation with 4fs timestep > > > > Joe Joe wrote: > > > Hi, > > > > > > I get good conservation when running NVE in gromacs with 4 fs when I > use > > > PME-switch for electrostatics but not so good when I use switch. Any > > > thoughts why that would be? Params shown below. > > > > Finite cutoffs (such as used with "switch") are intrinsically unlikely > > to conserve energy. > > > > Mark > > That is not right. > Finite cut-off's such as switch and shift are purposely designed to > conserve energy. > Switch is not particularly good though, since the switching introduces > large forces. > I would advise to use PME-switch or reaction-field-zero for electrostatics > and shift for vdw. > > But the main problem in your setup seems to be the 0.1 nm buffer between > the cut-off > and rlist. In general you will need a buffer of 0.25 to 0.3 nm. > You can use rlist=-1 to get exact integration and then vary rlist to get a > reasonable > neighborlist update frequency (somewhere around 10 steps). > We should automate the choice of rlist such that the user does not need to > worry > about this. > > Berk > > > > > -- > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] Energy Conservation with 4fs timestep
> Date: Wed, 1 Apr 2009 14:15:05 +1100 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Energy Conservation with 4fs timestep > > Joe Joe wrote: > > Hi, > > > > I get good conservation when running NVE in gromacs with 4 fs when I use > > PME-switch for electrostatics but not so good when I use switch. Any > > thoughts why that would be? Params shown below. > > Finite cutoffs (such as used with "switch") are intrinsically unlikely > to conserve energy. > > Mark That is not right. Finite cut-off's such as switch and shift are purposely designed to conserve energy. Switch is not particularly good though, since the switching introduces large forces. I would advise to use PME-switch or reaction-field-zero for electrostatics and shift for vdw. But the main problem in your setup seems to be the 0.1 nm buffer between the cut-off and rlist. In general you will need a buffer of 0.25 to 0.3 nm. You can use rlist=-1 to get exact integration and then vary rlist to get a reasonable neighborlist update frequency (somewhere around 10 steps). We should automate the choice of rlist such that the user does not need to worry about this. Berk _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Energy Conservation with 4fs timestep
Joe Joe wrote: Hi, I get good conservation when running NVE in gromacs with 4 fs when I use PME-switch for electrostatics but not so good when I use switch. Any thoughts why that would be? Params shown below. Finite cutoffs (such as used with "switch") are intrinsically unlikely to conserve energy. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Energy Conservation with 4fs timestep
Hi, I get good conservation when running NVE in gromacs with 4 fs when I use PME-switch for electrostatics but not so good when I use switch. Any thoughts why that would be? Params shown below. Thanks, Ilya ; ; File 'mdout.mdp' was generated ; By user: ichorny (502) ; On host: master.simprota.com ; At date: Tue Mar 31 18:01:39 2009 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.004 nsteps = 25 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm_mode= linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm_grps= system ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file nstxtcout= 5000 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.1 ; OPTIONS FOR ELECTROSTATICS AND VDW; Method for doing electrostatics coulombtype = pme-switch rcoulomb-switch = .85 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 80 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = .85 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; 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 = 1.e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = no ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t
