[gmx-users] Fatal Equilibration Errors

Sat Aug 8 21:33:17 CEST 2009

Hello,

I have successfully minimised and equilibrated ethylene glycol in a water
box.  I have noticed that there seem to be no hydrogen bonds between the
solute and solvent, but there are hydrogen bonds forming and breaking
between solvent molecules.  Is this a normal behavior during minimsation and
equilibration?

I am now trying to run MD on glycerol.  I start with a "glycerol.mol2" file
which contains the structure of glycerol.  I am using the following commands
to setup and run minimisation and equilibration on glycerol:

$ .../topolbuild1_2_1/src/topolbuild -n glycerol -dir
.../topolbuild1_2_1/dat/gromacs -ff gmx53a6

I modified the "defaults" part of the "ffglycerol.itp" (generated by
topolbuild) file to read:

===========================
[ defaults ]
;nbfunc     comb-rule      gen-pairs     fudgeLJ      fudgeQQ
      1             1             no         1.0          1.0
===========================

$ editconf -f glycerol.gro -o glycerol_box.gro -box 2.65 2.65 2.65
$ genbox -cp glycerol_box.gro -cs spc216.gro -o glycerol_solv.gro -p
glycerol.top -box 2.65 2.65 2.65
$ grompp -f em.mdp -c glycerol_solv.gro -p glycerol.top -o em.tpr

my "em.mdp" file is as follows:

===========================
constraints         =  none
integrator          =  steep
nsteps              =  10000

emtol               =  10.0
emstep              =  0.01

nstlist             =  2
coulombtype         =  PME
nstcomm             =  2

ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.3
nstxout             =  2

pbc                 =  xyz
pme_order           =  4
===========================

$ mdrun -v -deffnm em

the last few lines of output are:

===============================================================
Step= 6990, Dmax= 4.7e-04 nm, Epot= -3.34590e+04 Fmax= 9.13695e+01, atom= 4
Step= 6992, Dmax= 2.8e-04 nm, Epot= -3.34590e+04 Fmax= 1.40130e+02, atom= 5
Step= 6993, Dmax= 3.4e-04 nm, Epot= -3.34591e+04 Fmax= 8.57813e+01, atom= 4
Step= 6994, Dmax= 4.0e-04 nm, Epot= -3.34591e+04 Fmax= 2.41887e+02, atom= 5
Step= 6995, Dmax= 4.8e-04 nm, Epot= -3.34592e+04 Fmax= 9.36159e+01, atom= 4
Step= 6999, Dmax= 7.3e-05 nm, Epot= -3.34592e+04 Fmax= 4.95606e+01, atom= 4
Step= 7006, Dmax= 1.4e-06 nm, Epot= -3.34592e+04 Fmax= 4.89221e+01, atom= 4
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 7007 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -3.3459230e+04
Maximum force     =  4.9560604e+01 on atom 4
Norm of force     =  3.4399371e+00
===============================================================

As I believe these forces to be acceptable, I proceed to equilibration:

$ grompp -f nvt.mdp -c em.gro -p glycerol.top -o nvt.tpr

where my "nvt.mdp" file is:

===========================
title        = Glycerol NVT equilibration
define        = -DPOSRES

integrator    = md
nsteps        = 5000
dt        = 0.002

nstxout        = 10
nstvout        = 10
nstenergy    = 10
nstlog        = 10

continuation    = no
constraint_algorithm = lincs
constraints    = all-angles
lincs_iter    = 1
lincs_order    = 4

ns_type        = grid
nstlist        = 5
rlist        = 1.0
rcoulomb    = 1.0
rvdw        = 1.3

coulombtype    = PME
pme_order    = 4
fourierspacing    = 0.16

tcoupl        = V-rescale
tc-grps        = GOL SOL
tau_t        = 0.1 0.1
ref_t        = 300 300

pcoupl        = no

pbc        = xyz

DispCorr    = EnerPres

gen_vel        = yes
gen_temp    = 300
gen_seed    = -1
===========================

where "GOL" refers to GlycerOL.

$ mdrun -v -deffnm nvt

When I execute the above command, I get numerous errors of the following
type:

===============================================================
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.326337, max 0.500490 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
starting mdrun 'glycerol.pdb in water'
5000 steps,     10.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.663850, max 1.227203 (between atoms 1 and 7)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      1      3  172.3    0.2091   0.1644      0.2004
      7      9  164.1    0.2082   0.1625      0.2004
      2      3  124.5    0.1022   0.0787      0.1000
      1      2  148.3    0.1477   0.0882      0.1435
      5      6   30.4    0.0992   0.1265      0.1000
      8      9  134.1    0.1014   0.0660      0.1000
      7      8  138.2    0.1476   0.0991      0.1435

Warning: 1-4 interaction between 2 and 7 at distance 6.002 which is larger
than the 1-4 table size 2.300 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 0.004 ps: Water molecule starting at atom 1234 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

There were 12 inconsistent shifts. Check your topology
Segmentation fault
===============================================================

I don't know what is happening wrong.  Please advise.

Thank you.

Nancy
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