[gmx-users] continuation, gmx-users Digest, Vol 102, Issue 99

[Ali Alizadeh]

Dear Justin

In your opinion, Why did not i get a symmetric results of number density?

this is my md.mdp file:

title		= OPLS
define		= 	;
; Run parameters
integrator	= md		;
nsteps		= 1000000		;
dt		= 0.001		;
emtol		= 10.0
emstep          = 0.00001
; Output control
nstxout		= 10		;
nstvout		= 10		;
nstenergy	= 10		;
nstlog		= 10		;
nstxtcout       = 10
xtc_precision   = 10
; Bond parameters
continuation	= no		;
constraint_algorithm = lincs	;
constraints	= all-bonds	;
lincs_iter	= 1		;
lincs_order	= 4		;
; Neighborsearching
ns_type		= grid		;
nstlist		= 1		;
rlist		= 1.0		;
rcoulomb	= 1.0		;
rvdw		= 1.0		;
; Electrostatics
coulombtype	= PME		;
pme_order	= 4		;
fourierspacing	= 0.16		;
ewald_geometry  = 3d
; Temperature coupling is on
tcoupl		= berendsen	;
tc-grps		= System	;
tau_t		= 0.1	;
ref_t		= 240	;
; Pressure coupling is on
pcoupl		= berendsen	;
pcoupltype	= isotropic	;
tau_p		= 2.0		;
ref_p		= 300.0		;
compressibility = 4.5e-5	;
refcoord_scaling = com
; Periodic boundary conditions
pbc		= xyz		; 3-D PBC
; Dispersion correction
DispCorr	= EnerPres	;
; Velocity generation
gen_vel		= no		;



-- 
Sincerely