Hello,
I am trying to simulate a 133 residue protein with a RNA
dinucleotide. I modelled the complexed, minimized it and trying to start
the simulation with some contraints on the complex. But the system refuses
to proceed, despite the following measures:
a) Changing tol from 0.000001 to 0.0001
b) Chaning number of processors to one (look at the densities).
(I also looked at densities for different cut-offs (7-8A) but all of then
fall at the same initial value ~0.7)
But none seems to work. One complex comes out at first step itself and the
second one comes out after a fraction of a pico second.
Help please!
Thanks a lot,
-Sanjeev
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
NSTEP = 350 TIME(PS) = 0.700 TEMP(K) = 64.56 PRESS = 56.46
Etot = -49955.0009 EKtot = 1913.3991 EPtot = -51868.4000
BOND = 117.3860 ANGLE = 491.2637 DIHED = 789.7539
1-4 NB = 454.2161 1-4 EEL = 1011.7866 VDWAALS = 7723.0118
EELEC = -62718.0513 EHBOND = 0.0000 CONSTRAINT = 262.2331
EAMBER (non-constraint) = -52130.6331
EKCMT = 1348.7518 VIRIAL = 1118.9030 VOLUME = 188549.8422
Density = 0.7831
Ewald error estimate: 0.5425E-04
------------------------------------------------------------------------------
COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
DEVIATION IS TOO LARGE
NITER, NIT, LL, I AND J ARE : 0 0 125 256 257
-------------------------------------------------------------------------------
Input file
-------------------------------------------------------------------------------
First phase of equlibriation
&cntrl
imin=0,
ntr=1,
ntx=1, irest=0,
ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
ntf=2, ntb=2, igb=0, scnb=2.0, scee=1.2,
cut=10.0,
nstlim=2500, ndfmin=6, ntcm=1, dt=0.002,
tempi=0., temp0=100., ntt=1, tautp=0.5, dtemp=0.,
ntp=1, taup=0.5, npscal=1,
ntc=2, tol=0.001,
/
&ewald
vdwmeth=1,
/
group no 1
1000
RES 1 135
END
END
Received on Sun Sep 02 2001 - 05:56:12 PDT
