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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