Minimization does not converge

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Thu Nov 11 2010 - 17:42:42 CST

Hi all,

I am trying to carry out a minimization of y2a.pdb/y2a.psf for exercise 3 (Mutation of tyrosine into alanine) of the FEP tutorial.

I run the minimization conf. file and quickly end up iterating ad infinitum with the following screen output:

LINE MINIMIZER BRACKET: DX 0 0 DU nan nan DUDX nan nan nan
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU nan nan DUDX nan nan nan
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU nan nan DUDX nan nan nan
LINE MINIMIZER REDUCING GRADIENT FROM nan TO nan
LINE MINIMIZER BRACKET: DX 0 0 DU nan nan DUDX nan nan nan

This suggests that atoms clash heavily that the minimization never converges.

However, my pdb file does not contain atoms with identical coordinates:

ATOM 1 CAY ALA Y 1 -6.510 1.800 3.000 1.00 0.00 Y2A C
ATOM 2 HY1 ALA Y 1 -7.600 1.800 3.000 1.00 0.00 Y2A H
ATOM 3 HY2 ALA Y 1 -6.146 2.827 3.000 1.00 0.00 Y2A H
ATOM 4 HY3 ALA Y 1 -6.146 1.286 3.890 1.00 0.00 Y2A H
ATOM 5 CY ALA Y 1 -5.959 1.086 1.764 1.00 0.00 Y2A C
ATOM 6 OY ALA Y 1 -6.723 0.604 0.929 1.00 0.00 Y2A O
ATOM 7 N ALA Y 1 -4.625 1.022 1.653 1.00 0.00 Y2A N
ATOM 8 HN ALA Y 1 -4.042 1.434 2.366 1.00 0.00 Y2A H
ATOM 9 CA ALA Y 1 -3.981 0.373 0.528 1.00 0.00 Y2A C
ATOM 10 HA ALA Y 1 -4.279 -0.675 0.493 1.00 0.00 Y2A H
ATOM 11 CB ALA Y 1 -4.375 1.038 -0.792 1.00 0.00 Y2A C
ATOM 12 HB1 ALA Y 1 -5.061 1.862 -0.594 1.00 0.00 Y2A H
ATOM 13 HB2 ALA Y 1 -3.483 1.420 -1.288 1.00 0.00 Y2A H
ATOM 14 HB3 ALA Y 1 -4.863 0.307 -1.437 1.00 0.00 Y2A H
ATOM 15 C ALA Y 1 -2.467 0.443 0.649 1.00 0.00 Y2A C
ATOM 16 O ALA Y 1 -1.943 0.999 1.613 1.00 0.00 Y2A O
ATOM 17 N Y2A Y 2 -1.759 -0.126 -0.336 1.00 0.00 Y2A N
ATOM 18 HN Y2A Y 2 -2.238 -0.571 -1.106 1.00 0.00 Y2A H
ATOM 19 CA Y2A Y 2 -0.309 -0.126 -0.336 1.00 0.00 Y2A C
ATOM 20 HA Y2A Y 2 0.055 0.902 -0.336 1.00 0.00 Y2A H
ATOM 21 CBA Y2A Y 2 0.242 -0.840 0.900 1.00 0.00 Y2A C
ATOM 22 HB1A Y2A Y 2 -0.586 -1.194 1.515 1.00 0.00 Y2A H
ATOM 23 HB2A Y2A Y 2 0.852 -1.687 0.589 1.00 0.00 Y2A H
ATOM 24 CGA Y2A Y 2 1.087 0.121 1.702 1.00 0.00 Y2A C
ATOM 25 CD1A Y2A Y 2 1.256 1.440 1.261 1.00 0.00 Y2A C
ATOM 26 HD1A Y2A Y 2 0.777 1.772 0.340 1.00 0.00 Y2A H
ATOM 27 CE1A Y2A Y 2 2.040 2.331 2.004 1.00 0.00 Y2A C
ATOM 28 HE1A Y2A Y 2 2.171 3.357 1.661 1.00 0.00 Y2A H
ATOM 29 CZA Y2A Y 2 2.654 1.904 3.187 1.00 0.00 Y2A C
ATOM 30 OHA Y2A Y 2 3.416 2.769 3.909 1.00 0.00 Y2A O
ATOM 31 HHA Y2A Y 2 3.463 3.644 3.516 1.00 0.00 Y2A H
ATOM 32 CD2A Y2A Y 2 1.702 -0.306 2.885 1.00 0.00 Y2A C
ATOM 33 HD2A Y2A Y 2 1.570 -1.332 3.227 1.00 0.00 Y2A H
ATOM 34 CE2A Y2A Y 2 2.486 0.585 3.627 1.00 0.00 Y2A C
ATOM 35 HE2A Y2A Y 2 2.964 0.253 4.548 1.00 0.00 Y2A H
ATOM 36 CBB Y2A Y 2 0.242 -0.840 0.900 1.00 0.00 Y2A C
ATOM 37 HB1B Y2A Y 2 -0.586 -1.194 1.515 1.00 0.00 Y2A H
ATOM 38 HB2B Y2A Y 2 0.852 -1.687 0.589 1.00 0.00 Y2A H
ATOM 39 HB3B Y2A Y 2 1.087 0.121 1.702 1.00 0.00 Y2A H
ATOM 40 C Y2A Y 2 0.242 -0.840 -1.572 1.00 0.00 Y2A C
ATOM 41 O Y2A Y 2 -0.522 -1.322 -2.407 1.00 0.00 Y2A O
ATOM 42 C ALA Y 3 3.734 -1.483 -2.686 1.00 0.00 Y2A C
ATOM 43 O ALA Y 3 4.258 -0.927 -1.723 1.00 0.00 Y2A O
ATOM 44 NT ALA Y 3 4.442 -2.052 -3.672 1.00 0.00 Y2A N
ATOM 45 HNT ALA Y 3 3.963 -2.496 -4.442 1.00 0.00 Y2A H
ATOM 46 CAT ALA Y 3 5.892 -2.052 -3.672 1.00 0.00 Y2A C
ATOM 47 HT1 ALA Y 3 6.256 -1.538 -2.782 1.00 0.00 Y2A H
ATOM 48 HT2 ALA Y 3 6.256 -1.538 -4.561 1.00 0.00 Y2A H
ATOM 49 HT3 ALA Y 3 6.256 -3.079 -3.672 1.00 0.00 Y2A H
ATOM 50 N ALA Y 3 1.576 -0.904 -1.683 1.00 0.00 Y2A N
ATOM 51 HN ALA Y 3 2.159 -0.492 -0.969 1.00 0.00 Y2A H
ATOM 52 CA ALA Y 3 2.220 -1.553 -2.808 1.00 0.00 Y2A C
ATOM 53 HA ALA Y 3 1.922 -2.601 -2.843 1.00 0.00 Y2A H
ATOM 54 CB ALA Y 3 1.826 -0.888 -4.128 1.00 0.00 Y2A C
ATOM 55 HB1 ALA Y 3 1.140 -0.064 -3.930 1.00 0.00 Y2A H
ATOM 56 HB2 ALA Y 3 2.718 -0.506 -4.624 1.00 0.00 Y2A H
ATOM 57 HB3 ALA Y 3 1.338 -1.619 -4.772 1.00 0.00 Y2A H
END

Any help as to what might be causing this?

Here is the configuration file used: Please note that I do not want PME nor do I want PBC hence the commented areas

Thanks in advance

###################################################
# MINIMIZATION
###################################################

# INPUT

parameters par_all27_prot_lipid.prm
paraTypeCharmm on

exclude scaled1-4
1-4scaling 1.0

# TOPOLOGY

structure y2a.psf

# COORDINATES

coordinates y2a.pdb

# INITIAL TEMPERATURE

temperature 300.0

# CELL

#cellbasisvector1 26 0 0
#cellbasisvector2 0 26 0
#cellbasisvector3 0 0 26
#cellorigin 0 0 0

# OUTPUT FREQUENCIES

outputenergies 100
outputtiming 100
outputpressure 100
restartfreq 100
XSTFreq 100

# OUTPUT AND RESTART

outputname minimize_0
restartname minimize

binaryoutput no
binaryrestart yes

# PME

PME no
PMETolerance 10e-6
PMEInterpOrder 4

PMEGridSizeX 35
PMEGridSizeY 35
PMEGridSizeZ 35

# WRAP WATER FOR OUTPUT

wrapAll off

# CONSTANT-T

langevin on
langevinTemp 300.0
langevinDamping 1.0

# CONSTANT-P

LangevinPiston off
LangevinPistonTarget 1.0
LangevinPistonPeriod 100
LangevinPistonDecay 100
LangevinPistonTemp 300

#StrainRate 0.0 0.0 0.0
useGroupPressure no

useflexiblecell no

# SPACE PARTITIONING

#splitpatch hydrogen
#hgroupcutoff 2.8
#stepspercycle 20
#margin 1.0

# CUT-OFFS

switching on
switchdist 8.0
cutoff 9.0
pairlistdist 10.0

# RESPA PROPAGATOR

timestep 0.5
fullElectFrequency 2
nonbondedFreq 1

# SHAKE

rigidbonds all
rigidtolerance 0.000001
rigiditerations 400

# COM

commotion no

# MINIMIZE

minimize 2000

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