[gmx-users] nstcalclr bug?
Andrea.Spitaleri at iit.it
Thu Oct 24 19:14:11 CEST 2013
Thanks! I get confused because mdout.mdp was different from the output of gmxdump.
Messaggio inviato dal mio ASUS MeMO Pad
Mark Abraham <mark.j.abraham at gmail.com> ha scritto:
Ja. No twin-range => no long-range :-)
On Thu, Oct 24, 2013 at 5:50 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
> I think nstcalclr would only do something if you have longer range
> interactions to calculate (lr means longer than rlist). Therefore
> something has be longer than rlist for this to happen.
> > Hi there,
> > I am using gromacs-4.6.1 with this mdp file:
> > integrator = md ; leap-frog integrator
> > nsteps = 3000000 ; 6.0 ns
> > dt = 0.002 ; 2 fs
> > nstxout = 0 ; save coordinates every 10 ps
> > nstvout = 0 ; save velocities every 10 ps
> > nstenergy = 5000 ; save energies every 10 ps
> > nstlog = 5000 ; update log file every 5 ps
> > nstcalcenergy = 100 ;
> > nstxtcout = 5000 ; xtc every 10 ps
> > xtc_precision = 100
> > continuation = yes ; Restarting
> > constraint_algorithm = lincs ; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 20 ; 10 fs
> > rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> > rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> > nstcalclr = 10
> > cutoff-scheme = Group
> > vdwtype = Cut-off
> > vdw-modifier = Potential-shift
> > coulombtype = PME ; Particle Mesh Ewald for long-range
> > pme_order = 4 ; cubic interpolation
> > fourierspacing = 0.16 ; grid spacing for FFT
> > coulomb-modifier = Potential-shift
> > tcoupl = V-rescale ; modified Berendsen thermostat
> > tc-grps = System ; two coupling groups - more
> > tau_t = 0.1 ; time constant, in ps
> > ref_t = 300 ; reference temperature, one for each
> group, in K
> > energygrps = complex Water ; group(s) to write to energy file
> > pcoupl = Parrinello-Rahman ; Pressure coupling on in
> > pcoupltype = isotropic ; uniform scaling of box vectors
> > tau_p = 2.0 ; time constant, in ps
> > ref_p = 1.0 ; reference pressure, in bar
> > compressibility = 4.5e-5 ; isothermal compressibility of water,
> > refcoord_scaling = com
> > pbc = xyz ; 3-D PBC
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> > gen_vel = no ; Velocity generation is off
> > gen-seed = 128742
> > ; number of steps for center of mass motion removal
> > nstcomm = 1000
> > the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says
> > nstcalclr = 0. If I set rvdw = 1.4 (> rlist), gmxdump of the file tpr is
> > now correct to nstcalclr = 10.
> > I have double checked the manual but I couldn't find the reason of this
> > behaviour.
> > is this a bug or am I doing wrong somewhere??
> > thanks for any helps
> > and
> > Andrea Spitaleri PhD
> > D3 - Drug Discovery & Development
> > Istituto Italiano di Tecnologia
> > Via Morego, 30 16163 Genova
> > cell: +39 3485188790
> > --
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