Thanks
Input Parameters:
integrator = md
nsteps = 100000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 10
nstxout = 500
nstvout = 1000
nstfout = 0
nstenergy = 10
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 = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = V-rescale
epc = Berendsen
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 1.01325e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.01325e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01325e+00}
compress (3x3):
compress[ 0]={ 4.50000e-03, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 4.50000e-03, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-03}
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 = Cut-off
rcoulomb_switch = 0
rcoulomb = 1.4
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
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: 11297
ref_t: 300
tau_t: 0.1
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: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1 Coulomb: 1.4 LJ: 1.4
System total charge: -0.000
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Removing pbc first time
Initializing LINear Constraint Solver
The number of constraints is 5500
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 5600 Atoms
Max number of connections per atom is 4
Total number of connections is 11000
Max number of graph edges per atom is 4
Total number of graph edges is 11000
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 4.85e-05
Initial temperature: 307.706 K
Started mdrun on node 0 Fri Oct 9 11:09:36 2009
Step Time Lambda
0 0.00000 0.00000
Grid: 7 x 7 x 7 cells
Energies (kJ/mol)
LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) Potential
4.09130e+05 -2.61414e+01 -1.20894e+04 -4.35981e+02 3.96578e+05
Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd ()
4.24944e+04 4.39073e+05 9.04819e+02 -1.31995e+04 4.03210e-04
Step 1 Warning: pressure scaling more than 1%, mu: 0.960399 0.960399
0.960399
Step 3 Warning: pressure scaling more than 1%, mu: 1.13142 1.13142 1.13142
Step 4 Warning: pressure scaling more than 1%, mu: 1.81135 1.81135 1.81135
Step 5 Warning: pressure scaling more than 1%, mu: 3.4866e+09
3.4866e+09 3.4866e+09
-------------------------------------------------------
Program mdrun, VERSION 4.0.2
Source code file: constr.c, line: 136
Fatal error:
Too many LINCS warnings (5235)
If you know what you are doing you can adjust the lincs warning
threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
On Thu, Oct 8, 2009 at 3:05 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Yongchul Chung wrote:
Hi guys,
As Justin pointed out, it was the problem with md simulation
blowing up. I also had coloumbtype=PME and had to switch to
cut-off to make my simulation run faster.
And it will be substantially less accurate than using PME. I would
say Jochen's advice is the best - reduce the time step to something
reasonable, and use PME.
-Justin
Thanks for all the help.
On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub
<joc...@xray.bmc.uu.se <mailto:joc...@xray.bmc.uu.se>
<mailto:joc...@xray.bmc.uu.se <mailto:joc...@xray.bmc.uu.se>>>
wrote:
delta_t = 0.01
You are using a 10 fs timestep!!! That is way too long.
Standard is
2 (with bond constraints).
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane
molecules but
keep receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax < 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force = 4.4903098e+02 on atom 172
Norm of force = 3.0003010e+01
Then I performed mdrun with the output of this file and gets
LINCS warning:
Input Parameters:
integrator = md
nsteps = 8000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 10
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy = 10
nstxtcout = 0
init_t = 0
delta_t = 0.01
xtcprec = 1000
nkx = 125
nky = 125
nkz = 125
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 = V-rescale
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 = 2
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: 11297
ref_t: 300
tau_t: 0.1
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: 2
System total charge: -0.000
Generated table with 1500 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1500 data points for LJ12.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Removing pbc first time
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E.
M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 5500
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion
removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
There are: 5600 Atoms
Max number of connections per atom is 4
Total number of connections is 11000
Max number of graph edges per atom is 4
Total number of graph edges is 11000
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining:
6.33e-04
Initial temperature: 306.393 K
Started mdrun on node 0 Thu Oct 8 09:58:49 2009
Step Time Lambda
0 0.00000 0.00000
Grid: 25 x 25 x 25 cells
-------------------------------------------------------
Program mdrun, VERSION 4.0.2
Source code file: constr.c, line: 136
Fatal error:
Too many LINCS warnings (3821)
If you know what you are doing you can adjust the lincs
warning
threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
-------------------------------------------------------
Can anyone help me to navigate this issue?
Thanks
-- Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve
University
------------------------------------------------------------------------
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-- ---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
---------------------------------------------------
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--
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
------------------------------------------------------------------------
_______________________________________________
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before
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--
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
