[gmx-users] nstcalclr bug?

[Andrea Spitaleri]

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