AMBER: time-averaged restraints

From: John <john.dalmaris.imperial.ac.uk>
Date: Fri, 14 May 2004 18:04:49 +0100

Hello,

I have been attempting to run an NMR refinement simulated annealing. I tried
the standard way with no time-averaged restraints (instantaneous) which
worked fine. When tried the time-averaged (input file can be found in
http://dumb.ch.ic.ac.uk/~john/share/SA/) I get this at the beginning of the
simulation:


 NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 0.00 PRESS = 0.0
 Etot = -32901.4768 EKtot = 0.0208 EPtot = -32901.4976
 BOND = 44.0211 ANGLE = 56.0840 DIHED = 140.0414
 1-4 NB = -34.9194 1-4 EEL = -31247.8230 VDWAALS = -4904.0965
 EELEC = 3033.9212 EHBOND = 0.0000 RESTRAINT = 11.2737
 EAMBER (non-restraint) = -32912.7713
 Ewald error estimate: 0.8953E-03
 
---------------------------------------------------------------------------- 
--
============================================================================
===
                      NMR restraints for step      9
 Energy (this step): Bond =   11.262   Angle =     0.000   Torsion =
0.011
 Energy (tot. run) : Bond =   10.086   Angle =     0.000   Torsion =
0.010
 DEVIATIONS:    Target=(r2+r3)/2                 Target = closer of r2/r3
            This step         Entire run        This step        Entire run
           ave.    rms       ave.    rms       ave.    rms      ave.     rms
 Bond      1.767   1.823     1.767   1.823     0.800   0.800     0.800
0.800
 Angle     0.000   0.000     0.000   0.000     0.000   0.000     0.000
0.000
 Torsion 165.000 165.000   165.000 165.000   106.429 106.486   106.429
106.486
============================================================================
===
 NSTEP =     10 TIME(PS) =     0.010  TEMP(K) =   325.61  PRESS =     0.0
 Etot   =  -28039.9418  EKtot   =    4840.2583  EPtot      =  -32880.2001
 BOND   =      43.9056  ANGLE   =      56.1462  DIHED      =     140.0501
 1-4 NB =     -34.9133  1-4 EEL =  -31247.8857  VDWAALS    =   -4904.0883
 EELEC  =    3034.0176  EHBOND  =       0.0000  RESTRAINT  =      32.5677
 EAMBER (non-restraint)  =  -32912.7677
 Ewald error estimate:   0.8945E-03
 
----------------------------------------------------------------------------
--
============================================================================
===
                      NMR restraints for step     10
 Energy (this step): Bond =   32.568   Angle =     0.000   Torsion =
0.000
 Energy (tot. run) : Bond =   12.334   Angle =     0.000   Torsion =
0.009
 DEVIATIONS:    Target=(r2+r3)/2                 Target = closer of r2/r3
            This step         Entire run        This step        Entire run
           ave.    rms       ave.    rms       ave.    rms      ave.     rms
 Bond      2.767   2.803     1.867   1.921     1.800   1.800     0.900
0.900
 Angle     0.000   0.000     0.000   0.000     0.000   0.000     0.000
0.000
 Torsion 325.668 325.777   181.067 181.078   267.097 267.322   122.495
122.570
============================================================================
===
The Temperature rises rapidly.
I have also tried the same system in vacuum and again while it works fine
without implementing the time-averaged restraints, upon implementing them
the rapid increase of the temperature occurs at the same time step and
getting this error message:
Frac coord min, max:   -2.10318734371480D-003  0.500000000000000     
 The system has extended beyond 
     the extent of the virtual box.
 Restarting sander will recalculate
    a new virtual box with 30 Angstroms
    extra on each side, if there is a
    restart file for this configuration.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error
I have tried various TAUTP and decay parameters but still getting the same
problem.
Has anyone used time-averaged restraints that can provide a helping hand?
Thanks for the help.
Bets wishes,
John
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Received on Fri May 14 2004 - 18:53:00 PDT
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