[gmx-users] nstcalclr bug?

[jkrieger at mrc-lmb.cam.ac.uk]

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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