[gmx-users] some problems by freshman
zpxu
zp.xu at mf.mpg.de
Thu Aug 15 22:04:04 CEST 2002
I have set exclusions to 3, and delete the [nonbond_params] section in my
'nt_nb.itp'.
then I get the results:
--------------------------------------------------------------
There are 0 atoms for free energy perturbation
Input Parameters:
integrator = steep
nsteps = 100
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart = FALSE
bShakeSOR = FALSE
etc = No
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}
bSimAnn = FALSE
zero_temp_time = 0
rlist = 1
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
DispCorr = No
fudgeQQ = 1
free_energy = no
init_lambda = 0
sc_alpha = 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
em_stepsize = 0.01
em_tol = 100
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
bd_temp = 300
bd_fric = 0
ld_seed = 1993
cos_accel = 0
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 1197
ref_t: 0
tau_t: 0
acc: 0 0 0
nfreeze: N N N
energygrp_excl[ 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
CPU= 0, lastcg= 399, targetcg= 200, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 400
nsb->natoms: 400
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 400 400 400
Max number of bonds per atom is 3
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 1 molecules, 400 charge groups and 400 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 4804.41
Started Steepest Descents on node 0 Thu Aug 15 21:51:32 2002
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance = 1.00000e+02
Number of steps = 100
Grid: 40 x 40 x 100 cells
Step Time Lambda Annealing
0 0.00000 0.00000 0.00000
Energies (kJ/mol)
Morse G96Angle LJ (SR) Coulomb (SR) Potential
3.69421e+01 5.48292e+05 -3.97362e+03 0.00000e+00 5.44355e+05
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Step Time Lambda Annealing
1 1.00000 0.00000 0.00000
Energies (kJ/mol)
Morse G96Angle LJ (SR) Coulomb (SR) Potential
7.78185e+02 5.47780e+05 -5.03171e+03 0.00000e+00 5.43527e+05
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Step Time Lambda Annealing
2 2.00000 0.00000 0.00000
......
Step Time Lambda Annealing
99 99.00000 0.00000 0.00000
Energies (kJ/mol)
Morse G96Angle LJ (SR) Coulomb (SR) Potential
7.10715e+04 2.96588e+05 -4.01797e+03 0.00000e+00 3.63642e+05
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Step Time Lambda Annealing
100 100.00000 0.00000 0.00000
Steepest Descents did not converge in 100 steps
Potential Energy = 3.63642e+05
Maximum force: 1.05288e+04
M E G A - F L O P S A C C O U N T I N G
RF=Reaction-field Free=Free Energy SC=Softcore
T=Tabulated S=Solvent W=Water WW=Water-Water
Computing: M-Number M-Flop's % Flop's
LJ 4.057560 125.784360 44.5
Innerloop-Iatom 0.040400 0.404000 0.1
NS-Pairs 6.378092 133.939932 47.4
Reset In Box 0.040400 0.363600 0.1
Shift-X 0.040400 0.242400 0.1
CG-CoM 0.040400 1.171600 0.4
Angles 0.106050 17.286150 6.1
Morse Potent. 0.056055 3.251190 1.2
Virial 0.002727 0.049086 0.0
Total 282.49232 100.0
NODE (s) Real (s) (%)
Time: 1.000 1.000 100.0
Finished mdrun on node 0 Thu Aug 15 21:51:33 2002
----------------------------------------------------------------------------
--
I am wondering such fundamental things:
1) I want L-J interaction only between the C_I(innertube) and C_O(outertube)
atoms (two type of atoms in one molecule).
and their are four sections concern L-J potential.
a)section [atomtypes] in topology file
b)section [nonbond_params] in topology file
c)section [pairtypes] in topology file
d)section [pairs] in topology file
now I only use b).
is it ok?
2) the unit of potential parameters, I use nm,kJ/mol
is it ok?
3) my coordinate is at nanometer scale, so I shift it by 3nm, let the tubes
in box.
4) I set charge to zero, and set charge group arbitrarily.
More information about the gromacs.org_gmx-users
mailing list