Subject: help about charmm

From: wei <[email-masked]>
Date: Fri, 10 Jan 2003 09:15:56 -0500

Hi,all:

I am simulating a "peptide in chloroform" system using charmm. and I want to see if one specific conformation could be kept in the simulation. so during the minimization and 
equilibration, I constrained the dihedral angles to keep the conformation, and before starting the dynamic run, I released the constraint and let the system go.but after about 
300ps,the running was broken and charmm gave out following error message. could any body tell me what is the matter?I will attach the error message and input file.

1)input file:
****************************************
................................(omitted the psf and coordinates reading parts)

!nonbond interaction options

NBONDS ATOM EWALD PMEWALD KAPPA 0.32  FFTX 30 FFTY 30 FFTZ 30 ORDER 6 -
        CUTNB 12.0  CTOFNB 10.0  VDW  VSHIFT  

! impose periodic boundary conditions:

set L  30.0

crystal define cubic @L @L @L 90.0 90.0 90.0
crystal build noper 0 cutoff 12.0

image byres XCEN 0.0 YCEN 0.0 ZCEN 0.0 select segid SOLV end
image byres XCEN 0.0 YCEN 0.0 ZCEN 0.0 select segid ANTA end
update inbfrq 1 imgfrq 1

SHAKE BONH TOLERANCE 1.0e-6 para

set p e116

title
* dynamics equilibration phase
*

! set up output

open read unit 30 card name output/@p_eq3.rst
open unit 50 card write name output/@p_dyn.stt
open unit 61 card write name output/@p_dyn.rst
open unit 60 unfo write name output/@p_dyn.cor
open unit 62 unfo write name output/@p_dyn.vel

! heat system by MD : assign velocities from Gaussian distribution
! at progeressively higher temepratures

DYNAMICS LEAP VERLET RESTART NSTEP 1000000 TIMESTEP 0.001 -
  IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 5000 -
  KUNIT 50 IUNWRI 61 IUNREAD 30 IUNCRD 60 IUNVEL 62 -
  imgfrq 25 inbfrq 25 ihbfrq 0 -
  NPRINT 100  NSAVC 10 NSAVV  10 

open write card unit 11 name crd/e116_dyn.pdb
write coor pdb card unit 11
close unit 11

OPEN UNIT 38 CARD WRITE NAME crd/e116_dyn.crd
WRITE COOR CARD UNIT 38
CLOSE UNIT 38

stop

***************************************************************

2)error message:
**************************************************8
 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE
 NITER=    0 LL=   24 I=   45 J=   46
 TOLER=      0.9940090000 DIFF=   -118.6741615914 RRPR=     -3.0523892808
  X(I)          -1.0072591014        1.3202935338       -1.3045016708
  XREF(I)       -0.1732638907        1.1171361155      -12.5019766435
  X(J)          -0.8531869062        0.4484378605      -12.2079093966
  XREF(J)       -0.8449202314        0.4550922027      -12.1785811928
 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE
 NITER=    1 LL=   24 I=   45 J=   46
 TOLER=      0.9940090000 DIFF=    -29.4221023014 RRPR=     -1.5388717892
  X(I)          -1.0021304050        1.2912715351       -1.6674501432
  XREF(I)       -0.1732638907        1.1171361155      -12.5019766435
  X(J)          -0.9244544165        0.8517227173       -7.1644379164
  XREF(J)       -0.8449202314        0.4550922027      -12.1785811928
 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE
 NITER=    2 LL=   24 I=   45 J=   46
 TOLER=      0.9940090000 DIFF=     -7.1151444645 RRPR=     -0.7945813248
  X(I)          -0.9996083068        1.2769996176       -1.8459344280
  XREF(I)       -0.1732638907        1.1171361155      -12.5019766435
  X(J)          -0.9595010735        1.0500429052       -4.6842500420
  XREF(J)       -0.8449202314        0.4550922027      -12.1785811928
 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE
 NITER=    3 LL=   24 I=   45 J=   46
 TOLER=      0.9940090000 DIFF=     -1.5607449339 RRPR=     -0.4459900113
  X(I)          -0.9984270723        1.2703153099       -1.9295282321
  XREF(I)       -0.1732638907        1.1171361155      -12.5019766435
  X(J)          -0.9759153106        1.1429269312       -3.5226444725
  XREF(J)       -0.8449202314        0.4550922027      -12.1785811928
 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE
 NITER=    4 LL=   24 I=   45 J=   46
 TOLER=      0.9940090000 DIFF=     -0.2383717583 RRPR=     -0.3097583685
  X(I)          -0.9979654386        1.2677030410       -1.9621972081
  XREF(I)       -0.1732638907        1.1171361155      -12.5019766435
  X(J)          -0.9823300961        1.1792265834       -3.0686818265
  XREF(J)       -0.8449202314        0.4550922027      -12.1785811928
 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE
 NITER=    5 LL=   24 I=   45 J=   46
 TOLER=      0.9940090000 DIFF=     -0.0115266923 RRPR=     -0.2798010496
  X(I)          -0.9978639254        1.2671286035       -1.9693811113
  XREF(I)       -0.1732638907        1.1171361155      -12.5019766435
  X(J)          -0.9837407065        1.1872088718       -2.9688555049
  XREF(J)       -0.8449202314        0.4550922027      -12.1785811928
 ** ERROR IN SHAKEA ** DEVIATION IN SHAKE TOO LARGE
 NITER=    6 LL=   24 I=   45 J=   46
 TOLER=      0.9940090000 DIFF=     -0.0000330333 RRPR=     -0.2781973369
  X(I)          -0.9978584911        1.2670978520       -1.9697656890
  XREF(I)       -0.1732638907        1.1171361155      -12.5019766435
  X(J)          -0.9838162211        1.1876361896       -2.9635114775
  XREF(J)       -0.8449202314        0.4550922027      -12.1785811928
 TOTAL ENERGY CHANGE EXCEEDED
     20.     KCAL AND 10% OF THE TOTAL KINETIC ENERGY IN THE LAST STEP
 PREVIOUS E =     542.1     CURRENT E =    0.1297E+07 KINETIC =    0.5518E+07
 WRIDYN: RESTart file was written at step  800176

      ***** LEVEL -2 WARNING FROM <DYNAMC> *****
      ***** ENERGY CHANGE TOLERANCE EXCEEDED
      ******************************************
      BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS  5

**************************************************************************************************************