[gmx-users] frustrating NVE
Xiaobing Feng
xbfeng05 at yahoo.com.cn
Thu Nov 10 23:42:02 CET 2005
Dear everyone,
I did a MD NVE run. The total energy is going up nearly linearly,
total energy went from -46000 kJ/mol to -45700 kJ/mol after 450 ps, and no sign
to level off. There is no close contacts in the conf.gro, and the run is pretty
long, the system should be equilibrated long ago. The system is made of a solid
and its melt, an interfacial system.
The main setting is :
dt =1fs, Coulombtype=PME, rlist = rvdw = rcoulomb=1.2, fourierspacing=0.1,
pme_order=4, ewald_rtol=1e-5
There is one H atom, O-H bond is contrainted by Lincs.
Given in the following is the complete mdout.mdp ( I removed comments only).
Could anybody tell me what's wrong with my setting?
Thanks a lot.
Xiaobing
---------------mdout.mdp -----------------------
cpp = /usr/bin/cpp
include =
define =
integrator = md
tinit = 0
dt = 0.001
nsteps = 500000
init_step = 0
comm-mode = Linear
nstcomm = 1
comm-grps =
bd-fric = 0
ld-seed = 1993
emtol = 10
emstep = 0.01
nstcgsteep = 1000
nbfgscorr = 10
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstcheckpoint = 10000
nstlog = 1000
nstenergy = 100
nstxtcout = 2000
xtc-precision = 10000
xtc-grps =
energygrps =
nstlist = 1
ns_type = grid
pbc = xyz
rlist = 1.2
domain-decomposition = no
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.2
epsilon_r = 1
epsilon_rf = 1
vdw-type = Cut-off
rvdw-switch = 0
rvdw = 1.2
DispCorr = EnerPres
table-extension = 1
energygrp_table =
fourierspacing = 0.1
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
Tcoupl = no
tc-grps = System
tau_t = 0.1
ref_t = 309
Pcoupl = no
Pcoupltype = semiisotropic
tau_p = 2.0
compressibility = 4.4395e-5 4.4395e-5
ref_p = 1.01325 1.01325
andersen_seed = 815131
QMMM = no
QMMM-grps =
QMmethod =
QMMMscheme = normal
QMbasis =
QMcharge =
QMmult =
SH =
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
MMChargeScaleFactor = 1
bOPT =
bTS =
annealing =
annealing_npoints =
annealing_time =
annealing_temp =
gen_vel = yes
gen_temp = 309
gen_seed = 1993
constraints = hbonds
constraint-algorithm = Lincs
unconstrained-start = no
Shake-SOR = no
shake-tol = 1e-04
lincs-order = 5
lincs-iter = 2
lincs-warnangle = 30
morse = no
energygrp_excl =
disre = No
disre-weighting = Conservative
disre-mixed = no
disre-fc = 1000
disre-tau = 0
nstdisreout = 100
orire = no
orire-fc = 0
orire-tau = 0
orire-fitgrp =
nstorireout = 100
dihre = No
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-power = 1
sc-sigma = 0.3
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
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