[gmx-users] charge group moved too far between two domain decomposition steps?
Dear all,I am intrigued by the error that I have received this morning, as follows:The charge group starting at atom 37920 moved more than the distance allowed by the domain decomposition (1.40) in direction Ydistance out of cell 7.144197Old coordinates: 54.499 39.697 14.058New coordinates: 54.499 39.697 14.058Old cell boundaries in direction Y: 19.468 32.846New cell boundaries in direction Y: 18.667 32.553If the charge group moved, if any, then shouldn't the new coordinates be showing different values?It was a new NPT calculation that I continued from a 20ns NVT run, so it should be equilibrated well enough, for a simple water on graphene system.Using GROMACS 5.0, I was unable to start the NPT with Berendsen thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my tau-T was 0.5, following the general rule of thumb, that tau-P should be larger than tau-T to allow thermal degrees of freedom to equilibrate faster than the box size).Should I reduce tau-P?Below is my NPT.mdp parameters:; RUN CONTROL PARAMETERSintegrator= mdtinit = 2.000dt= 0.002 ; 2 fsnsteps = 500 ; 10,000 pscomm-mode= Linearnstcomm = 10emtol = 0.001niter = 30; OUTPUT CONTROL OPTIONSnstxout = 5000 ; save coordinates every 8 psnstvout = 5000 ; save velocities every 8 psnstfout = 0nstlog = 5000 ; update log file every 8 psnstenergy= 5000 ; save energies every 8 ps;nstxtcout is replaced with nstxout-compressednstxout-compressed= 5000 ; no. of steps between writing coordinates using lossy compression;xtc-precision is replaced with compressed-x-precisioncompressed-x-precision = 3000 ; precision with which to write to the compressed trajectory file; Periodic boundary conditions: xyz (default), no (vacuum)cutoff-scheme = Verlet ; default for GROMACS-5.0nstlist = 1 ; A smaller nstlist may reduce LINCS warningsns-type = grid ;pbc = xyz;periodic_molecules= yes ; cannot be used with SHAKE; nblist cut-offrlist = 1.40 ; short-range neighbourlist cutoffnstcalclr= 1coulombtype = PMEcoulomb-modifier = Potential-shift-Verletr_coulomb= 1.40 ; short-range electrostatic cutoffrcoulomb-switch = 0 ; used when potential-switch (coulomb-modifier) is specifiedepsilon-r= 1 ; default value=1pme_order= 4fourierspacing = 0.12fourier_nx= 0fourier_ny= 0fourier_nz= 0ewald_rtol= 1e-05ewald_geometry = 3depsilon_surface = 0 ; Use 0 when simulation is done with PME;vdw-type = switch is replaced with the following two flags in GROMACS-5.0vdwtype = Cut-offvdw_modifier = Potential-switch; cut-off lengthsrvdw-switch = 1.00rvdw = 1.40 ; short-range van der Waals cutoffconstraints = noneconstraint-algorithm = SHAKEcontinuation = yes ; starting from NVT runShake-SOR= noshake-tol= 0.0001;lincs-order = 4 ; accuracy of LINCS;lincs-iter= 24 ; also related to accuracy; Lincs will write a warning to the stderr if in one step a bond; rotates over more degrees than;lincs-warnangle = 30Tcoupl = v-rescalenh-chain-length = 1 ; the leapfrog md integrator only supports 1; Groups to couple separatelytc-grps = GRA SOL; Time constant (ps) and reference temperature (K)tau-t = 0.5 0.5ref-t = 300 300nsttcouple= 20 ; added by k-wong ; not specified in Yanbin's MDPPcoupl = Parrinello-RahmanPcoupltype= isotropic; Time constant (ps), compressibility (1/bar) and reference P (bar)tau-p = 5.0 ; time constant in pscompressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1ref-p = 1.0 ; reference pressure, in bar; Non-equilibrium MD stufffreezegrps= GRAfreezedim= Y Y Ygen_vel = no;gen_temp = 300;gen_seed = 173529Thanks in advance!Regards,Kester -- 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] charge group moved too far between two domain decomposition steps?
Hi, You should start by using a time step more appropriate to your use of constraints = none, or vice versa. Mark On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong kester2...@ibs.re.kr wrote: Dear all, I am intrigued by the error that I have received this morning, as follows: The charge group starting at atom 37920 moved more than the distance allowed by the domain decomposition (1.40) in direction Y distance out of cell 7.144197 Old coordinates: 54.499 39.697 14.058 New coordinates: 54.499 39.697 14.058 Old cell boundaries in direction Y: 19.468 32.846 New cell boundaries in direction Y: 18.667 32.553 If the charge group moved, if any, then shouldn't the new coordinates be showing different values? It was a new NPT calculation that I continued from a 20ns NVT run, so it should be equilibrated well enough, for a simple water on graphene system. Using GROMACS 5.0, I was unable to start the NPT with Berendsen thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my tau-T was 0.5, following the general rule of thumb, that tau-P should be larger than tau-T to allow thermal degrees of freedom to equilibrate faster than the box size). Should I reduce tau-P? Below is my NPT.mdp parameters: ; RUN CONTROL PARAMETERS integrator = md tinit= 2.000 dt = 0.002; 2 fs nsteps = 500 ; 10,000 ps comm-mode= Linear nstcomm = 10 emtol= 0.001 niter= 30 ; OUTPUT CONTROL OPTIONS nstxout = 5000; save coordinates every 8 ps nstvout = 5000; save velocities every 8 ps nstfout = 0 nstlog = 5000; update log file every 8 ps nstenergy= 5000; save energies every 8 ps ;nstxtcout is replaced with nstxout-compressed nstxout-compressed = 5000; no. of steps between writing coordinates using lossy compression ;xtc-precision is replaced with compressed-x-precision compressed-x-precision = 3000; precision with which to write to the compressed trajectory file ; Periodic boundary conditions: xyz (default), no (vacuum) cutoff-scheme= Verlet ; default for GROMACS-5.0 nstlist = 1 ; A smaller nstlist may reduce LINCS warnings ns-type = grid ; pbc = xyz ;periodic_molecules = yes ; cannot be used with SHAKE ; nblist cut-off rlist= 1.40 ; short-range neighbourlist cutoff nstcalclr= 1 coulombtype = PME coulomb-modifier = Potential-shift-Verlet r_coulomb= 1.40 ; short-range electrostatic cutoff rcoulomb-switch = 0 ; used when potential-switch (coulomb-modifier) is specified epsilon-r= 1 ; default value=1 pme_order= 4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 ; Use 0 when simulation is done with PME ;vdw-type = switch is replaced with the following two flags in GROMACS-5.0 vdwtype = Cut-off vdw_modifier = Potential-switch ; cut-off lengths rvdw-switch = 1.00 rvdw = 1.40 ; short-range van der Waals cutoff constraints = none constraint-algorithm = SHAKE continuation = yes; starting from NVT run Shake-SOR= no shake-tol= 0.0001 ;lincs-order = 4 ; accuracy of LINCS ;lincs-iter = 24; also related to accuracy ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than ;lincs-warnangle = 30 Tcoupl = v-rescale nh-chain-length = 1; the leapfrog md integrator only supports 1 ; Groups to couple separately tc-grps = GRA SOL ; Time constant (ps) and reference temperature (K) tau-t= 0.5 0.5 ref-t= 300 300 nsttcouple = 20 ; added by k-wong ; not specified in Yanbin's MDP Pcoupl = Parrinello-Rahman Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 5.0 ; time constant in ps compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ref-p= 1.0 ; reference pressure, in bar ; Non-equilibrium MD stuff freezegrps = GRA freezedim= Y Y Y gen_vel = no ;gen_temp = 300 ;gen_seed = 173529
