Hi Markus, It means that I should change cutoff to the Shift, right (manual 7.3.10)
jes On Sat, 05 Apr 2008 Markus Miettinen wrote : >Hi Jes, > > > to me it seems that you have rlist = rvdw: > >>nstlist = 10 >>rlist = 1.0 >>rvdw = 1.0 > > > This will lead to a loss of energy, because between list updates > two particles originally at distance, say, 1.01 from each other > can easily move within rvdw from each other, but they will not > "see" each other until the lists are updated again. > > In other words, you have particles moving within the attractive > LJ-potential region without giving them the speed-up that the > attractive potential should provide. This mistake equals loss of > energy, and becomes apparent in NVE. In NVT the thermostat > (artificially!) fixes the energy loss. > > The correct way is to set rlist > rvdw. > > >Cheers, >markus. > >-- >Halli delendum est. > >On Apr 3, 2008, at 13:00 , [EMAIL PROTECTED] wrote: > >>Date: 3 Apr 2008 08:12:40 -0000 >> From: "JMandumpal" <[EMAIL PROTECTED]> >>Subject: Re: Re: [gmx-users] NVT and NVE >>To: "Discussion list for GROMACS users" <[email protected]> >>Message-ID: <[EMAIL PROTECTED]> >>Content-Type: text/plain; charset="iso-8859-1" >> >>Dear David, >> >>I post the input file for the NVE run. >> >>I use SHAKE, Would it be better if I use LINCS? >> >>title = NVE >>cpp = /usr/bin/cpp >>; RUN CONTROL PARAMETERS >>integrator = md >>; Start time and timestep in ps >>tinit = 500 >>dt = 0.0015; >>nsteps = 360000; 540 ps >>; For exact run continuation or redoing part of a run >>init_step = 0 >>; number of steps for center of mass motion removal >>nstcomm = 1 >>; group(s) for center of mass motion removal >>comm-grps = SOL >>; OUTPUT CONTROL OPTIONS >>; Output frequency for coords (x), velocities (v) and forces (f) >>nstxout = 0 >>nstvout = 0 >>nstfout = 0 >>; Checkpointing helps you continue after crashes >>nstcheckpoint = 1000 >>; Output frequency for energies to log file and energy file >>nstlog = 100000 >>nstenergy = 1000 >>; Output frequency and precision for xtc file >>nstxtcout = 0 >>xtc-precision = 1000 >>; select multiple groups. By default all atoms will be written. >>; NEIGHBORSEARCHING PARAMETERS >>nstlist = 10 >>; ns algorithm (simple or grid) >>ns_type = grid >>; Periodic boundary conditions: >>pbc = xyz >>; nblist cut-off >>rlist = 1.0 >>; OPTIONS FOR ELECTROSTATICS AND VDW >>; Method for doing electrostatics >>coulombtype = pme >>rcoulomb = 1.0 >>ewald_rtol = 1e-5 ; since erfc(sigma*rcutoff) =ewald_rtol >>optimize_fft = yes >>; Relative dielectric constant for the medium >>epsilon_r = 1 ; for water >>; Method for doing Van der Waals >>vdw-type = cut-off >>rvdw = 1.0 >>; Spacing for the PME/PPPM FFT grid >>fourierspacing = 0.12 ; >>; EWALD/PME/PPPM parameters >>pme_order = 4 >>ewald_geometry = 3d >>epsilon_surface = 0 >>; OPTIONS FOR WEAK COUPLING ALGORITHMS >>; Temperature coupling >>Tcoupl = no >>Pcoupl = no >>; GENERATE VELOCITIES FOR STARTUP RUN >>gen_vel = no >>gen-temp = 300 >>gen-seed = 173529 >>; OPTIONS FOR BONDS >>constraints = all-bonds >>constraint_algorithm = shake >>shake_tol = 0.0001 >>morse = no >> >> >>rgds, >>Jes
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