[gmx-users] nstcalclr bug?

[Andrea Spitaleri]

Thanks! I get confused because mdout.mdp was different from the output of gmxdump.

And


Messaggio inviato dal mio ASUS MeMO Pad

Mark Abraham <mark.j.abraham at gmail.com> ha scritto:


Ja. No twin-range => no long-range :-)

Mark


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)
> constrained
> > 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
> electrostatics
> > 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
> accurate
> > 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
> NPT
> > 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,
> bar^-1
> > 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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