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>> 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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