st wrote:
Hi,
I now minimized the energy before the mdrun, and still got the same
problem. I also tried several other things:
1. I mdrun the system without water, it runs fine. But once I added
water, it stops propagating steps/files while still seems running.
2. The system has nonzero charge of 0.9, and the Coulomb energy seems
(very high) the major contribution to the total energy.
Any suggestion will be appreciated!
I would address #2 first. What is the cause of a net charge of 0.9? This
magnitude of charge is non-negligible. What force field are you using? I seem
to recall multiple people having non-zero charges when they used OPLS-AA with
"zwitterion" as the termini (which is wrong for a full protein). Could this be
part of your problem?
-Justin
below is the output of a recent try:
____________________________________________________________________________________________________________________________________________________________________
Input Parameters:
integrator = md
nsteps = 40000
init_step = 0
ns_type = Grid
nstlist = 1
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 100
nstenergy = 100
nstxtcout = 100
init_t = 0
delta_t = 0.0005
xtcprec = 1e+06
nkx = 50
nky = 50
nkz = 80
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Nose-Hoover
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}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
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
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
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: 59322
ref_t: 300
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
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
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 --- -------- --------
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: -0.900
Generated table with 4000 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ12.
Tabscale = 2000 points/nm
Enabling SPC water optimization for 6481 molecules.
Configuring nonbonded kernels...
Testing ia32 SSE2 support... present.
Removing pbc first time
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 19775 Atoms
Max number of connections per atom is 37
Total number of connections is 53706
Max number of graph edges per atom is 4
Total number of graph edges is 26788
Initial temperature: 0 K
Started mdrun on node 0 Wed Sep 9 10:52:42 2009
Step Time Lambda
0 0.00000 0.00000
Grid: 8 x 8 x 12 cells
Energies (kJ/mol)
Bond Morse Angle G96Angle Proper Dih.
3.89303e+02 1.05091e+01 6.55879e+01 7.38907e+00 1.17177e+03
Ryckaert-Bell. LJ (SR) Coulomb (SR) Coul. recip. Potential
-3.77214e+00 2.37518e+01 -2.87848e+05 -2.00200e+04 -3.06203e+05
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
6.24804e+02 -3.05578e+05 -3.05578e+05 2.53350e+00 -8.53815e+03
________________________________________________________________________________________________________________________________________________________
--------------------------------------------------
From: "Justin A. Lemkul" <[email protected]>
Sent: Tuesday, September 01, 2009 4:35 PM
To: "Discussion list for GROMACS users" <[email protected]>
Subject: Re: [gmx-users] mdrun running without simulating new steps
st wrote:
Hi,
I run a two-molecule system with mdrun_d in a water box (~10000
water molecules.)
The program looks running properly (no errors nor warnnings)
However the program seems stop outputting files (because the output
file size stop increases) after about 5min.
The mdrun_d interface looks normal without any errors, the md.log
contains only two saves:
<snip>
Grid: 9 x 9 x 14 cells
Energies (kJ/mol)
Bond Morse Angle G96Angle
Proper Dih.
3.35232e+05 3.27635e+01 7.09937e+02 1.73811e+01 2.47097e+03
LJ (SR) Coulomb (SR) Coul. recip. Potential
Kinetic En.
1.48669e+05 -4.50390e+05 -1.89304e+04 1.78117e+04 4.38796e+05
Total Energy Conserved En. Temperature Pressure (bar)
4.56608e+05 4.56608e+05 1.09892e+03 -5.74950e+04
Step Time Lambda
100 0.05000 0.00000
Energies (kJ/mol)
Bond Morse Angle G96Angle
Proper Dih.
3.38536e+05 1.06967e+03 2.21584e+04 4.26526e+01 3.13457e+03
LJ (SR) Coulomb (SR) Coul. recip. Potential
Kinetic En.
8.73487e+04 -5.64854e+05 -4.48577e+04 -1.57422e+05 3.56524e+05
Total Energy Conserved En. Temperature Pressure (bar)
1.99102e+05 7.60608e+05 8.92881e+02 7.56563e+04
I'd say the system is exploding. Your temperature is oscillating
between 1000 K and 893 K using a Nose-Hoover thermostat, and your
potential starts off in excess of 10^4 kJ mol^-1. Did you run any
sort of energy minimization or weak-coupling equilibration before this
run?
It's odd that mdrun wouldn't give some sort of LINCS warning or write
out step*.pdb files right beforehand, though.
-Justin
**********************
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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