[gmx-users] Lincs warning
Moeed
lecielll at googlemail.com
Thu Apr 29 03:03:30 CEST 2010
Dear gmx experts,
I am having problem doing MD run for a hydrocarbon system. The system
contains a stack of Hexane molecules using editconf.
The distance between molecuels in the box is more than 30 A. I am wondering
why I get large forces (system is blowing up) with this distance!. (LINCS
warning) with dt=0.002
Program mdrun, VERSION 4.0.7
Source code file: constr.c, line: 136
Fatal error:
Too many LINCS warnings (1053)
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
It seems Fmax, Epot values are reasonable. . In the list archive I read this
statement by Mr.Justin Lemskul:
"changing cutoffs haphazardly is a recipe for failure" but I have no idea
how this works....*
*
I also reduced the timestep to 0.001 ps but it did not work. I even did not
get those written pdb files I got from dt=0.002 I had a look at structures
and they were like rings!!. (initially hezane had a linear structure).
Thank you for your time and help in advance
*em output file:*
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 100
Step= 0, Dmax= 1.0e-02 nm, Epot= 8.36824e+05 Fmax= 2.26627e+03, atom=
2947
Step= 1, Dmax= 1.0e-02 nm, Epot= 8.17823e+05 Fmax= 2.98349e+03, atom=
2007
Step= 2, Dmax= 1.2e-02 nm, Epot= 7.87850e+05 Fmax= 2.24621e+03, atom=
2447
Step= 3, Dmax= 1.4e-02 nm, Epot= 7.70259e+05 Fmax= 3.13292e+03, atom=
3127
Step= 4, Dmax= 1.7e-02 nm, Epot= 7.50886e+05 Fmax= 2.87650e+03, atom=
3125
Step= 5, Dmax= 2.1e-02 nm, Epot= 7.15803e+05 Fmax= 5.48652e+03, atom=
3127
Step= 6, Dmax= 2.5e-02 nm, Epot= 6.59011e+05 Fmax= 2.97146e+03, atom=
3105
Step= 7, Dmax= 3.0e-02 nm, Epot= 7.10849e+05 Fmax= 5.51243e+03, atom=
3127^MStep= 8, Dmax= 1.5e-02 nm, Epot= 6.38805e+05 Fmax= 3.87761e+03,
atom= 3107
Step= 9, Dmax= 1.8e-02 nm, Epot= 6.21481e+05 Fmax= 2.69101e+03, atom=
1687
Step= 10, Dmax= 2.1e-02 nm, Epot= 6.43071e+05 Fmax= 5.74780e+03, atom=
227^MStep= 11, Dmax= 1.1e-02 nm, Epot= 6.00633e+05 Fmax= 2.56262e+03,
atom= 3107
Step= 12, Dmax= 1.3e-02 nm, Epot= 5.86914e+05 Fmax= 2.40254e+03, atom=
1687
Step= 13, Dmax= 1.5e-02 nm, Epot= 5.85431e+05 Fmax= 4.58696e+03, atom=
3107
Step= 14, Dmax= 1.9e-02 nm, Epot= 5.61423e+05 Fmax= 2.94308e+03, atom=
3127
Step= 15, Dmax= 2.2e-02 nm, Epot= 5.85550e+05 Fmax= 5.56128e+03, atom=
1827^MStep= 16, Dmax= 1.1e-02 nm, Epot= 5.43780e+05 Fmax= 1.91577e+03,
atom= 3107
Step= 17, Dmax= 1.3e-02 nm, Epot= 5.42825e+05 Fmax= 3.49456e+03, atom=
4247
Step= 18, Dmax= 1.6e-02 nm, Epot= 5.30046e+05 Fmax= 3.16969e+03, atom=
4247
Step= 19, Dmax= 1.9e-02 nm, Epot= 5.41307e+05 Fmax= 4.27646e+03, atom=
4247^MStep= 20, Dmax= 9.6e-03 nm, Epot= 5.14493e+05 Fmax= 1.28031e+03,
atom= 3115
Step= 21, Dmax= 1.2e-02 nm, Epot= 5.14984e+05 Fmax= 3.45692e+03, atom=
4247^MStep= 22, Dmax= 5.8e-03 nm, Epot= 5.07865e+05 Fmax= 1.27065e+03,
atom= 3115
Step= 23, Dmax= 6.9e-03 nm, Epot= 5.02771e+05 Fmax= 1.75304e+03, atom=
4247
Step= 24, Dmax= 8.3e-03 nm, Epot= 4.98096e+05 Fmax= 2.10118e+03, atom=
4247Step= 23, Dmax= 6.9e-03 nm, Epot= 5.02771e+05 Fmax= 1.75304e+03,
atom= 4247
Step= 24, Dmax= 8.3e-03 nm, Epot= 4.98096e+05 Fmax= 2.10118e+03, atom=
4247
Step= 25, Dmax= 1.0e-02 nm, Epot= 4.95017e+05 Fmax= 2.30502e+03, atom=
4247
Step= 26, Dmax= 1.2e-02 nm, Epot= 4.94561e+05 Fmax= 3.17535e+03, atom=
1847
Step= 27, Dmax= 1.4e-02 nm, Epot= 4.91526e+05 Fmax= 2.99909e+03, atom=
1847
Step= 28, Dmax= 1.7e-02 nm, Epot= 5.00763e+05 Fmax= 4.45550e+03, atom=
1847^MStep= 29, Dmax= 8.6e-03 nm, Epot= 4.76093e+05 Fmax= 9.86600e+02,
atom= 3115
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 30 steps
Potential Energy = 4.76092783832156e+05
Maximum force = 9.86600079729483e+02 on atom 3115
Norm of force = 5.33725886931530e+02
gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)
md parameter file:
title = Hexane
cpp = /lib/cpp
; Preprocessing
define = -DPOSRES
; Run control
integrator = md
dt = 0.001 ; ps !
nsteps = 5000 ; total 1.0 ps.
nstcomm = 1 ; frequency for center of mass motion
removal
; Output control
nstenergy = 10 ; frequency to write energies to energy
file. i.e., energies and other statistical data are stored every 10 steps
nstxout = 10 ; frequency to write
coordinates/velocity/force to output trajectory file
nstvout = 1000
nstfout = 1
;nstlog = 10 ; frequency to write energies to log file
; Neighbor searching
nstlist = 10 ; neighborlist will be updated at least
every 10 steps
;ns_type = grid
; Electrostatics/VdW
coulombtype = PME
vdw-type = cut-off
; Cut-off
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Temperature coupling Berendsen temperature coupling is on in two
groups
Tcoupl = berendsen
tc-grps = HEX ;sol
tau_t = 0.1 ;0.1
ref_t = 300 ;300
; Pressure coupling: Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Velocity generation Generate velocites is on at 300 K. Manual
p155
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = all-bonds
constraint-algorithm = lincs
pbc=xyz
topology file:
moleculetype ]
; Name nrexcl
HEX 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot
-0.18
2 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot
-0.3
3 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot
-0.42
4 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot
-0.54
5 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot
-0.66
6 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot
-0.84
7 opls_140 1 HEX H1 6 0.06 1.008 ; qtot
-0.78
8 opls_140 1 HEX H2 6 0.06 1.008 ; qtot
-0.72
9 opls_140 1 HEX H3 6 0.06 1.008 ; qtot
-0.66
10 opls_140 1 HEX H4 5 0.06 1.008 ; qtot
-0.6
11 opls_140 1 HEX H5 5 0.06 1.008 ; qtot
-0.54
12 opls_140 1 HEX H6 4 0.06 1.008 ; qtot
-0.48
13 opls_140 1 HEX H7 4 0.06 1.008 ; qtot
-0.42
14 opls_140 1 HEX H8 3 0.06 1.008 ; qtot
-0.36
15 opls_140 1 HEX H9 3 0.06 1.008 ; qtot
-0.3
16 opls_140 1 HEX H10 2 0.06 1.008 ; qtot
-0.24
17 opls_140 1 HEX H11 2 0.06 1.008 ; qtot
-0.18
18 opls_140 1 HEX H12 1 0.06 1.008 ; qtot
-0.12
19 opls_140 1 HEX H13 1 0.06 1.008 ; qtot
-0.06
20 opls_140 1 HEX H14 1 0.06 1.008 ; qtot
0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
1 18 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
1 19 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
1 20 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
2 3 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
2 16 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
2 17 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
3 4 1 1.540000e-01 4.000000e+05 1.540000e-01 4.000000e+05
3 14 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
3 15 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
4 5 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
4 12 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
4 13 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
5 6 1 1.530000e-01 4.000000e+05 1.530000e-01 4.000000e+05
5 10 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
5 11 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 7 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 8 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
6 9 1 1.090000e-01 4.000000e+05 1.090000e-01 4.000000e+05
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 14 1
1 15 1
2 5 1
2 12 1
2 13 1
3 6 1
3 10 1
3 11 1
3 18 1
3 19 1
3 20 1
4 7 1
4 8 1
4 9 1
4 16 1
4 17 1
5 14 1
5 15 1
6 12 1
6 13 1
7 10 1
7 11 1
8 10 1
8 11 1
9 10 1
9 11 1
10 12 1
10 13 1
11 12 1
11 13 1
12 14 1
12 15 1
13 14 1
13 15 1
14 16 1
14 17 1
15 16 1
15 17 1
16 18 1
16 19 1
16 20 1
17 18 1
17 19 1
17 20 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 18 1 1.120000e+02 4.000000e+02 1.120000e+02
4.000000e+02
2 1 19 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
2 1 20 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
18 1 19 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
18 1 20 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
19 1 20 1 1.080000e+02 4.000000e+02 1.080000e+02
4.000000e+02
1 2 3 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
1 2 16 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
1 2 17 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
3 2 16 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
3 2 17 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
16 2 17 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
2 3 4 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
2 3 14 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
2 3 15 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
4 3 14 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
4 3 15 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
14 3 15 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
3 4 5 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
3 4 12 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
3 4 13 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
5 4 12 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
5 4 13 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
12 4 13 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
4 5 6 1 1.130000e+02 4.000000e+02 1.130000e+02
4.000000e+02
4 5 10 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
4 5 11 1 1.100000e+02 4.000000e+02 1.100000e+02
4.000000e+02
6 5 10 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
6 5 11 1 1.090000e+02 4.000000e+02 1.090000e+02
4.000000e+02
10 5 11 1 1.060000e+02 4.000000e+02 1.060000e+02
4.000000e+02
5 6 7 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
5 6 8 1 1.110000e+02 4.000000e+02 1.110000e+02
4.000000e+02
5 6 9 1 1.120000e+02 4.000000e+02 1.120000e+02
4.000000e+02
7 6 8 1 1.080000e+02 4.000000e+02 1.080000e+02
4.000000e+02
7 6 9 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
8 6 9 1 1.070000e+02 4.000000e+02 1.070000e+02
4.000000e+02
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
18 1 2 3 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
1 2 3 4 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
2 3 4 5 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
3 4 5 6 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
4 5 6 7 3 3.600000e+02 5.000000e+00 3.000000e+00
3.600000e+02 5.000000e+00 3.000000e+00
[ system ]
; Name
HEX
[ molecules ]
; Compound #mols
HEX 256
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