[gmx-users] NVT problem

[Andres Ortega]

HI , Dear Gromacs Users, 

I´ve been trying to run a NVT simulation, in order to equilibrate my system(
POPC + IONCHANNEL + SOL_IONS and DOX( Drug Molecule), i have already run a
EM, with DFLEXIBLE, and when i´m trying to run the NVT.mdp, the usual
comment of Water cannot be settle appear

and this 

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 417295953701.842102, max 94388491386880.000000 (between atoms 7122 and
7123)
bonds that rotated more than 30 degrees:

according with previous post, this could be of a problem of the topol (DOX)
or problems with my mdp file, this is my .mdp , i was wondering if you could
help me and give me some advices to solve this 

Thanks in advance for your time and attention , Andres Ortega

title		= NVT equilibration for channel_dox 
define		= -DPOSRES -DPOSRES_DOX	; position restrain the protein and for DOX
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 5000000	; 2 * 500000 = 1 ns ;10ns
dt		    = 0.002		; 2 fs

cutoff-scheme = verlet   ;

; Output control
nstxout		= 1000		; save coordinates every 2 ps
nstvout		= 1000		; save velocities every 2 ps
nstenergy	= 1000		; save energies every 2 ps
nstlog		= 1000		; update log file every 2 ps

; Bond parameters
continuation	= no		    ; first dynamics run
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
; Neighborsearching
ns_type		= grid		; search neighboring grid cels
nstlist		= 10		    ; 10 fs
rlist		= 1.2		; short-range neighborlist cutoff (in nm)
rcoulomb	= 1.2		; short-range electrostatic cutoff (in nm)
rvdw		= 1.2		; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype	= PME		; Particle Mesh Ewald for long-range electrostatics
pme_order	= 4		    ; cubic interpolation
fourierspacing	= 0.16		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= V-rescale	            ; modified Berendsen thermostat
tc-grps		= Protein POPC DOX Water_and_ions 	; three coupling groups - more
accurate
tau_t		= 0.1	0.1		0.1   0.1        ; time constant, in ps
ref_t		= 310 	310		310   310	        ; reference temperature, one for each
group, in K
; Pressure coupling is off
pcoupl		= no 		; no pressure coupling in NVT
; Periodic boundary conditions
pbc		    = xyz		; 3-D PBC
; Dispersion correction
DispCorr	= EnerPres	; account for cut-off vdW scheme
; Velocity generation
gen_vel		= yes		; assign velocities from Maxwell distribution
gen_temp	= 310		; temperature for Maxwell distribution
gen_seed	= -1		; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm		= 1
comm-mode	= Linear
comm-grps	= Protein_POPC DOX Water_and_ions



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