AMBER: question about TGMD: vlimit exceeded for step

From: <xhu1.memphis.edu>
Date: Fri, 08 Apr 2005 15:31:10 -0500

Dear all,

I am trying to run TGMD for a system: a 124-residue protein in a
waterbox.

Using AMBER7, weighted TGTRMSD from 4.345 to 0, TGTMDMDFRC=10 or 5 or
1, restrain force applied on residue 3-122, job running OK. then I
tried to apply the restraint force on residue 81-86 only, to see if
the structure will go to the reference structure as well. AMBER7 seems
not be able to do this. I move to AMBER8. Here is the input file:
*****************************************************************
#Data collection at 298K
 &cntrl
  IMIN = 0,ntx=5,irest=1,
  ntpr=10, ntwr=500,
  ntb=1,ntr=0,
  ntf=2,ntc=2,
  cut=8.5, nscm = 1000,
  NSTLIM = 400000, DT = 0.002,
  NTWX=500, NTWV=500,NTWE=500,
  TEMP0 = 298.0, TEMPI=298.0, NTT=1, TAUTP=2.0,
  nmropt=1, itgtmd=1, tgtrmsd=4.345, tgtmdfrc=10.00,
  tgtrmsmask=":3-122", tgtfitmask=":81-86 & !.H=",
 &end
 &wt
  TYPE='TGTRMSD', istep1 =0, istep2 = 200000,
  value1 = 4.345, value2 = 0.3,
 &end
 &wt
  TYPE='TGTRMSD', istep1 =200001, istep2 = 400000,
  value1 = 0.3, value2 = 0.,
 &end
 &wt
   type="END",
 &end
 &rst
   iat(1)=0,
 &end
END
***********************************************************************

I got a problem: job stopped immediately, and gave the informatin as
following:

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

 NSTEP = 10 TIME(PS) = 360.020 TEMP(K) = 5403.88 PRESS
= 0.0
 Etot = 867849.0298 EKtot = 181470.7791 EPtot =
686378.2507
 BOND = 1342.9958 ANGLE = 1534.9087 DIHED =
1235.1722
 1-4 NB = 1138.3272 1-4 EEL = 5449.3066 VDWAALS =
9292.6310
 EELEC = -64101.8524 EHBOND = 0.0000 RESTRAINT =
730486.7616
 EAMBER (non-restraint) = -44108.5108
 Ewald error estimate: 0.2247E-04
Current RMSD from reference: 13.246
Current target RMSD: 4.345
 ----------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
0.000
=======================================================================
 vlimit exceeded for step 11 ; vmax = 21.4771801052079
 vlimit exceeded for step 12 ; vmax = 1952.41027295489

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 2 439 882 883

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
***********************************************************************

I noticed that the "Current RMSD from reference" is huge different
from the "Current target RMSD". Is my TGTMDFRC too large?? I decreased
this value to 5, then 1, after running several tens steps, jobs
stopped for the same reason too. I read some emails in the mailing
list. the value of TGTMDFRC between 1-5 or 1-10 should be OK. then
does my input file have a problem?

Thank you very much for your help!

Shawn


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Received on Fri Apr 08 2005 - 21:53:00 PDT
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