Re: Minimization does not converge

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Sat Nov 13 2010 - 19:37:37 CST

This is a common problem getting an FEP calculation started, as the
minimizer doesn't seem to understand that some of the atoms are not
supposed to interact with each other. You can get around this by
minimizing and doing a short equilibration on the target solute and the
solvent. That should get the system close enough that you can put the
reference solute back in and start your equilibration/FEP.
Regards,
     Jeff

On 11/11/2010 6:42 PM, Christian Jorgensen wrote:
> 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

-- 
======================================================================
Jeffrey J. Potoff			  jpotoff_at_chem1.eng.wayne.edu
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:21 CST