[gmx-users] NVE Energy drop in Mixed Precision 4.6.7

[Johnny Lu]

Hi.

The system has 9000 water and a ~160 aa amino acid and uses amber99SB-ildn.

After extensive NPT (300ns, 2ns ts), and then NVT equilibrium (300 ns, 2ns
ts), the NVE simulation still has energy drop, despite of the very small
time step.

Is double precision gromacs the only solution?

The mdp file is:

title           = NVT equilibration
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 29500000      ; 1 ns
dt              = 0.0002        ; 0.5 fs

;NVE
;nstcomm         = 500 ; remove center of mass motion to reduce energy and
temp. drift.
shake-tol       = 0.0000001     ; shake tolerance.
verlet-buffer-drift = -1


- Output control
;nstxout         = 20           ; save coordinates every 1.0 ps
;nstvout         = 4           ; save velocities every 1.0 ps
;nstfout                = 20
nstenergy       = 20           ; save energies every 1.0 ps

nstlog          = 1000          ; update log file every 0.2 ps
; Bond parameters
continuation    = yes           ; Restarting after NVT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 4             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 40            ; 10 fs
rlist           = 1.3           ; 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)
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 6             ; cubic interpolation
fourierspacing  = 0.1           ; grid spacing for FFT

; Temperature coupling is off
tcoupl          = no    ; modified Berendsen thermostat
; Pressure coupling is off
pcoupl          = no

refcoord_scaling = com
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = EnerPres      ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off
cutoff-scheme = Verlet

Thank you in advance.