Hi,
You should maybe show us a plot of the energy for more than just a few
picoseconds.
Nevertheless, from my experience the only way to obtain constant energy
in the NVE ensemblewas to use double precision.
Guillaume
On 10/06/2014 09:34 PM, Johnny Lu wrote:
The run was on 12 Xeon CPU with a GPU.
On Mon, Oct 6, 2014 at 3:03 PM, Johnny Lu <johnny.lu...@gmail.com> wrote:
here is the energy from nve1.edr
http://oi62.tinypic.com/2pqw70l.jpg
On Mon, Oct 6, 2014 at 3:01 PM, Johnny Lu <johnny.lu...@gmail.com> wrote:
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.
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