Thank you.
Nancy
===========ethanediol.top===========
;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "ffethanediol.itp"
[ moleculetype ]
; name nrexcl
EDO_ideal.pdb 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH2 1 EDO C1 1 0.00000 14.02700
; 0.0000000
2 OA 1 EDO O1 1 0.00000 15.99940
; 0.0000000
3 H 1 EDO HO1 1 0.00000 1.00800
; 0.0000000
4 CH2 1 EDO C2 2 0.00000 14.02700
; 0.0000000
5 OA 1 EDO O2 2 0.00000 15.99940
; 0.0000000
6 H 1 EDO HO2 2 0.00000 1.00800
; 0.0000000
; total molecule charge = 0.0000000
[ bonds ]
; ai aj funct b0 kb
1 4 2 0.15200 5430000. ; C1- C2
4 5 2 0.14350 6100000. ; C2- O2
5 6 2 0.10000 15700000. ; O2- HO2
1 2 2 0.14350 6100000. ; C1- O1
2 3 2 0.10000 15700000. ; O1- HO1
[ pairs ]
2 5 1 ; O1- O2
1 6 1 ; C1- HO2
4 3 1 ; C2- HO1
[ angles ]
; ai aj ak funct th0 cth
2 1 4 2 109.500 320.0000 ; O1- C1- C2
1 4 5 2 109.500 320.0000 ; C1- C2- O2
4 5 6 2 109.500 450.0000 ; C2- O2- HO2
1 2 3 2 109.500 450.0000 ; C1- O1- HO1
[ dihedrals ]
; ai aj ak al funct phi0 cp mult
2 1 4 5 1 0.000 2.530 3 ;
dih O1- C1- C2- O2
2 1 4 5 1 0.000 5.350 1 ;
dih O1- C1- C2- O2
1 4 5 6 1 0.000 1.260 3 ;
dih C1- C2- O2- HO2
4 1 2 3 1 0.000 1.260 3 ;
dih C2- C1- O1- HO1
; Include Position restraint file
; WARNING: Position restraints and distance restraints ought not be done
together
#ifdef POSRES
#include "posreethanediol.itp"
#endif
; Include water topology
#include "spce.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; title from mol2 input
EDO_ideal.pdb
[ molecules ]
; molecule name nr.
EDO_ideal.pdb 1
===========ethanediol.top===========
On Sat, Aug 8, 2009 at 7:46 PM, Nagy, Peter I. <pn...@utnet.utoledo.edu
<mailto:pn...@utnet.utoledo.edu>> wrote:
It is extremely surprising that you have not found solute-solvent
hydrogen bonds in aqueous solution. What is the O-C-C-O
conformation? If it is trans, then what do the OH hydrogens do?
If O-C-C-O is gauche, then existence of two internal hydrogen bonds
is possible, but it is
far from the quantum mechanically most stable form in the gas phase.
I think that at least one solute-solvent hydrogen bond should have
been seen. There are papers in the literature which do show
solute-solvent hydrogen bonds in water. The exciting question is:
there is one
H-O-C-C trans moiety in the gas phase, and the other H is H-bonded
to this oxygen, when the O-C-C-O skeleton is gauche. Then the
question of solvation is, whether this intramolecular hydrogen bond
is maintained or disrupts. In aqueous solution it may, whereas in
chloroform or CCl4 both OH may be internally H-bonded. Experiments
found 12% O-C-C-O trans and 88% O-C-C-O gauche conformers in aqueous
solution. Modeling should find what are the positions of the hydroxy
hydrogens.
If you really do not find solute-solvent hydrogen bonds, your
ethylene-glycol charges may be
questionable. What charge values did you use? A possibility is that
the glycol OH charges cannot compete with those of the water model
(SPC, TIPxP or what) in forming intermolecular hydrogen bonds.
Peter Nagy
The University of Toledo,
Toledo, OH 43606
-----Original Message-----
From: gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org> on behalf of Nancy
Sent: Sat 8/8/2009 3:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Fatal Equilibration Errors
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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