AMBER Archive (2002)

Subject: (no subject)

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Wed Aug 07 2002 - 04:07:21 CDT

Dear all,
I am running an MD simulation of a protein using the GB-SA model (amber7 on
a IBM-SP3 computer).
Unexpectedly, the simulation works fine when I let everything free to move.
Instead, when I define a subset
of residues allowed to move (ibelly=1) the residues of the belly shift more
the 60Angs apart from the rest
of the protein, with consequent blow up of the energy! Is it correct to use
belly with GB-SA?
The problem occurs both using single of more processors, as well as using
SGI instead of SP3.
It occurs also by using igb=1 only, and *not* igb=1, gbsa=1, saltcon=1 as
in the following input file.
Help is very appreciated,
Giulio Rastelli

Here is my input file:

DYNAMICS with GB-SA
  &cntrl
   nmropt=1,
   ibelly=1,
   imin=0, nstlim=100000, dt=0.002, temp0=300.0, ntt=1,
   ntx=1, ntpr=100,
   ntf=2, ntc=2, ntb=0, igb=1, gbsa=1, saltcon=0.1, cut=10.0, scee=1.2,
   nsnb=25, ntwx=100,
  &end
  &wt type='TEMP0', istep1=1,istep2=5000,value1=0.,
             value2=300., &end
  &wt type='END' &end
  &rst iat=0, &end
Belly 8A
RES 12
RES 16
RES 19
RES 37 49
RES 52
RES 59
RES 67 68
RES 81 105
RES 121 132
RES 138 144
RES 146
RES 152
RES 173 178
RES 214
RES 215 218
END
END

And here is a sample of output. After less than 1ps the EGB and ESURF

contributions go out of range, the same happens to BOND because the

bonds between the belly and non-belly atoms are broken:

NSTEP = 800 TIME(PS) = 1.600 TEMP(K) =********* PRESS = 0.0
  Etot = nan EKtot = 5020605.6000 EPtot = nan
  BOND = ************ ANGLE = 5113.4269 DIHED = 1090.6565
  1-4 NB = 260.5515 1-4 EEL = 3135.9864 VDWAALS = -611.0062
  EELEC = -5191.9635 EGB = nan RESTRAINT = 0.0000
  ESURF = nan