[gmx-users] testing Tip5p water
tuyusong
tuyusong at gmail.com
Tue Sep 2 20:19:16 CEST 2008
Dear all,
a similar problem was proposed in this list in 2002:
http://www.gromacs.org/pipermail/gmx-users/2002-August/002339.html
I cannot solve my problem, when testing tip5p in gromacs.
T( c) density((g/cm^3) -E(kcal/mol)
REF1 25.0 0.999 9.8676
REF2 25.0 0.984 9.682
my results 25.0 0.984 -7.907
(data published (REF1:JCP 112, p8910 (2000)),
REF2: J. Chem. Phys. 117(19):8892-8897. (2002)) )
I want to what results in the big difference above.
my main parameters:
a. 512 water molecules in NVT system from 1ns average collections
after 1ns equilibrium.
integrator = md
dt = 0.001
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.22
DispCorr = Ener ;
fourierspacing = 0.12
pme_order = 6
Tcoupl = Berendsen
tau_t = 0.5
ref_t = 298
Thanks a lot in advance!
Yusong
//////////////////////////////////////////////////////////////////////////
PS: here is md0.log:
CPU= 0, lastcg= 127, targetcg= 383, myshift= 2
CPU= 1, lastcg= 255, targetcg= 511, myshift= 2
CPU= 2, lastcg= 383, targetcg= 128, myshift= 2
CPU= 3, lastcg= 511, targetcg= 256, myshift= 2
nsb->shift = 2, nsb->bshift= 0
Listing Scalars
nsb->nodeid: 0
nsb->nnodes: 4
nsb->cgtotal: 512
nsb->natoms: 2560
nsb->shift: 2
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 640 128 128
1 640 640 256 256
2 1280 640 384 384
3 1920 640 512 512
parameters of the run:
integrator = md
nsteps = 1000000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 1500
nstxout = 250
nstvout = 250
nstfout = 250
nstenergy = 250
nstxtcout = 1000
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 24
nky = 24
nkz = 21
pme_order = 6
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bUncStart = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
andersen_seed = 815131
rlist = 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.22
epsilon_r = 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = Ener
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 3069
ref_t: 298
tau_t: 0.5
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Max number of connections per atom is 4
Total number of connections is 1536
Max number of graph edges per atom is 4
Total number of graph edges is 1024
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1.22
System total charge: 0.000
Generated table with 1110 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1110 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1110 data points for LJ12.
Tabscale = 500 points/nm
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Parallelized PME sum used.
PARALLEL FFT DATA:
local_nx: 6 local_x_start: 0
local_ny_after_transpose: 6 local_y_start_after_transpose 0
Removing pbc first time
Done rmpbc
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: System, initial mass: 9223.92
There are: 384 Atoms
There are: 256 VSites
---
P.O.800-204 Haiping Fang Group
Shanghai Institute of Applied Physics
Chinese Academy of Sciences, China (201800)
Send email to: <mailto:tuyusong at gmail.com> tuyusong at gmail.com
Tel: (int : +86 21 59554533), (loc : 21 59554533)
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