I am trying to simulate a peptide with the following sequence:
p = sequence { VAL PRO ILE VAL THR PTR ALA ALA NHE }
initial minimization of the peptide completed with no problems. However,
when I try to heat the molecule using the following input (see below), the
simulation completes, but the temperature goes completely out of whack. The
peptide falls apart upon heating. The first few steps are OK, but at around
NSTEP=1000, the temperature rises to 2519.20 K and gets progressively
higher.
I have attempted this heating phase with both implicit (both igb=1 and
igb=2) and explicit solvents (tip3p water), as well as different thermostats
(both Langevin and Berendsen), and all of these attempts gave the same
result. The temperature would increase to a ridiculous value and the peptide
would break apart. I've also attempted different cutoff values (cut=16 and
cut=999).
Could you please provide some feedback as to what this problem could be.
Here's a sample input for my heating protocol. The bolded parts are what I
modified!
md run-T raise
&cntrl
imin=0, irest=0, ntx=1,
nstlim=10000, dt=0.0005,
ntc=2, ntf=2,
*ntt=1, tautp=1.0,*
tempi=0., temp0=300.0,
*igb=1, ntb=0,*
*cut=999.0*,
ntwe=25, ntwx=25, ntpr=25,
&end
&wt
type='TEMP0', istep1=0, istep2=1000, value1=0.0, value2=30.0,
&end
&wt
type='TEMP0', istep1=1001, istep2=2000, value1=30.0, value2=60.0,
&end
&wt
type='TEMP0', istep1=2001, istep2=3000, value1=60.0, value2=90.0,
&end
&wt
type='TEMP0', istep1=3001, istep2=4000, value1=90.0, value2=120.0,
&end
&wt
type='TEMP0', istep1=4001, istep2=5000, value1=120.0, value2=150.0,
&end
&wt
type='TEMP0', istep1=5001, istep2=6000, value1=150.0, value2=180.0,
&end
&wt
type='TEMP0', istep1=6001, istep2=7000, value1=180.0, value2=210.0,
&end
&wt
type='TEMP0', istep1=7001, istep2=8000, value1=210.0, value2=240.0,
&end
&wt
type='TEMP0', istep1=8001, istep2=9000, value1=240.0, value2=270.0,
&end
&wt
type='TEMP0', istep1=9001, istep2=10000, value1=270.0, value2=300.0,
&end
&wt
type='END'
&end
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Received on Mon Mar 28 2011 - 12:30:03 PDT
