[gmx-users] Abnormal alignment of waters after NVT simulation

[Du Jiangfeng (BIOCH)]

Dear All,

I encountered a very weird result after performing NVT simulation, all the waters aligned in lines, and they look like crystal cells. How did it turn out like this by temperature coupling? The following is the nvt.mdp parameters:

; NVT equilibration 
define		= -DPOSRES	; position restrain the protein but free the waters and lipids
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 120000		; 0.025 * 120000 = 3 ns
dt		= 0.025		; 25 fs since this is coarse grained system with martini force field
; Output control
nstxout		= 100		; save coordinates every 2.5 ps
nstvout		= 100		; save velocities every 0.2 ps
nstenergy	= 100		; save energies every 0.2 ps
nstlog		= 100		; update log file every 0.2 ps
; Bond parameters
continuation	= yes		; first dynamics run
constraint_algorithm = LINCS	; holonomic constraints 
constraints	= none	; I suppose "none" is standard used in martini force field
lincs_iter	= 1		; accuracy of LINCS
lincs_order	= 4		; also related to accuracy
lincs_warnangle          = 30
; Neighborsearching
ns_type		= grid		; search neighboring grid cells
nstlist		= 10		; 250 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	= 0.12		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= berendsen	; modified Berendsen thermostat
tc-grps		= Protein Non-Protein	; two coupling groups - more accurate
tau_t		= 0.2	0.2	; time constant, in ps
ref_t		= 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
 

Which parameters should be blamed to cause such artificial result?

Thank you!

    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands