AMBER Archive (2009)
Subject: [AMBER] Problem in pb simulation, PB_Bomb

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Thu Jan 29 2009 - 03:08:22 CST

Previous message: Barbault Florent: "Re: [AMBER] atomic charge"
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Hi,
Hope every one is fine.
I am running an explicit water simulation using watercap with igb=10. The system contains about 11600 atoms. I have used the default values for &pb name list. Follwing is the input file.

&cntrl
  imin = 1,
  maxcyc = 600,
  ntmin = 2,
  igb = 10,
  ntb = 0,
  ntr = 1,
  ntpr = 10,
  ivcap = 0,
  cut = 12
&end
&pb
  maxitn = 1800
  npbverb = 1
&end
Hold the ALL PROTEIN ATOMS fixed
500.0
FIND
* * * *
SEARCH
RES 1 614
END
Hold the SUGAR RING fixed
100.0
FIND
C1 * * *
C2 * * *
C3 * * *
C4 * * *
C5 * * *
O5 * * *
SEARCH
RES 618
END
END

Here, first I want to minimize the cap only so we have restrains on rest of the atoms except the sugar ring. Now the simulation fails and the output file says (an excerpt from the original file)...

NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 0.0000E+00 N 1

BOND = 253.7979 ANGLE = 1866.3353 DIHED = 5598.6689
VDWAALS = 1255.2427 EEL = NaN EGB = 0.0000
1-4 VDW = 2974.2047 1-4 EEL = 25470.2433 RESTRAINT = 0.0000
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
  NB-update: atom-based nb list 53765
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
  NB-update: atom-based nb list 53765
PB warning in pb_miccg(): CG maxitn exceeded!

======== FDPB Summary ========

Do FDPB every 1 steps
Nonbonded Update
   residue cutoff is set to 12.0000000000000
   fdpb cutoff is set to 10.0000000000000
   sas cutoff is set to 10.0000000000000
   nonbonded cutoff is set to 10.0000000000000
Grid Constants
   Grid dimension 19 19 19
   Grid spacing set to 5.60000000000000
   Grid boundary
       -37.627 68.773
       -46.838 59.562
       -65.610 40.790

Dielectric Map
   A single spherical dielectric boundary is used
   Use probe-accessible surface definition
     Compute SAS every 5 steps
     Solvent probe radius 1.60000000000000
     Surface dots per atom 400
     Buried atom radii increment 0.800000000000000
     Threshhold for exposed atom 0.200000000000000
     Current SAS 0.000000000000000E+000

Boundary conditions
   sum of grid charges as independent DH spheres

Physical constants
   Solute dielectric constant : 1.00000000000000
   Solvent dielectric constant : 80.0000000000000
   Temperature (K) : 300.000000000000
   Ionic strength (mM) : 0.000000000000000E+000
   Debye-Huckel parameter (1/A): 0.000000000000000E+000

FD Solver Option
   Use Modified ICCG solver

Iteration data
   Maximum iterations : 1800
   Convergence criteria: 1.000000000000000E-003
   Iterations required : 1800
   Norm of the constant vector: NaN
   Norm of the residual vector: NaN
   Convergence achieved : NaN

PB warning in pb_miccg(): CG maxitn exceeded!

======== FDPB Summary ========

Do FDPB every 1 steps
Nonbonded Update
   residue cutoff is set to 12.0000000000000
   fdpb cutoff is set to 10.0000000000000
   sas cutoff is set to 10.0000000000000
   nonbonded cutoff is set to 10.0000000000000
Grid Constants
   Grid dimension 79 79 79
   Grid spacing set to 0.700000000000000
   Grid boundary
        -9.627 45.673
       -18.838 36.462
       -37.610 17.690

Dielectric Map
   A single spherical dielectric boundary is used
   Use probe-accessible surface definition
     Compute SAS every 5 steps
     Solvent probe radius 1.60000000000000
     Surface dots per atom 400
     Buried atom radii increment 0.800000000000000
     Threshhold for exposed atom 0.200000000000000
     Current SAS 0.000000000000000E+000

Boundary conditions
   electrostatic focus boundary condition

Physical constants
   Solute dielectric constant : 1.00000000000000
   Solvent dielectric constant : 80.0000000000000
   Temperature (K) : 300.000000000000
   Ionic strength (mM) : 0.000000000000000E+000
   Debye-Huckel parameter (1/A): 0.000000000000000E+000

FD Solver Option
   Use Modified ICCG solver

Iteration data
   Maximum iterations : 1800
   Convergence criteria: 1.000000000000000E-003
   Iterations required : 1800
   Norm of the constant vector: NaN
   Norm of the residual vector: NaN
   Convergence achieved : NaN

NSTEP ENERGY RMS GMAX NAME NUMBER
10 NaN NaN 0.0000E+00 N 1

BOND = NaN ANGLE = NaN DIHED = NaN
VDWAALS = 0.0000 EEL = NaN EGB = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = NaN
EAMBER = NaN
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
  NB-update: atom-based nb list 53765
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
PB warning in pb_miccg(): CG maxitn exceeded!
  NB-update: atom-based nb list 53765
PB warning in pb_miccg(): CG maxitn exceeded!
.
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   NSTEP ENERGY RMS GMAX NAME NUMBER
     20 NaN NaN 0.0000E+00 N 1

I saw this error in the archive and there it was suggested that one should update MAXNEI manually in the pb hearder file and then recompile the code, is that recommended? similarly... if I change the cutres, cutnb and cutfd values to something smaller than default, then I recieve "maxnbr too short" error. Moreover, even if the MAXNEI thing is sloved what are these warnings all about why the iterarions all the time exceed the max value... can you spot roughly, if not clearly, what might have gone wrong and what could be done to solve it...

Any help is desperately needed and highly appreciated !
Thanks,
Waqas.

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Previous message: Barbault Florent: "Re: [AMBER] atomic charge"
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AMBER Archive (2009)Subject: [AMBER] Problem in pb simulation, PB_Bomb

AMBER Archive (2009)
Subject: [AMBER] Problem in pb simulation, PB_Bomb