[AMBER] High Temperature at NSTEP = 0

From: Alessandra Lacetera <alessandra.lacetera.gmail.com>
Date: Tue, 22 Oct 2013 17:41:12 +0200

Hi,
I was analysing dynamic simulation results and I've noticed that every step
of the dynamic starts with a high temperature (more or less 400 K).
Consequently also the plot of the potential energy presents a very high
fluctuation.
These are the parameters I'm using for the dynamic and the plot resulted by
the simulation.

cat << EOF > ${MOL}_md${j}.in
PME equil_md
 &cntrl
imin=0, irest=0, ntx=1, ntrx=1,
ntt=1, temp0=300.0, tempi = 300.0, gamma_ln=0.0,
ntp=1, taup=2.0, vlimit = 20.0,
ntb=2, ntc=2, ntf=2,
restraint_wt=0.0, restraintmask=':1-143',
ibelly=0,
nstlim=10000, dt=0.002,
ntwe=100, ntwx=1000, ntpr=1000,
nmropt=0,
jfastw=0, nscm=1000,
/
&ewald
eedmeth=1,skinnb=1.0,dsum_tol=0.000001,
/
EOF

Is it a big deal to start a simulation with a temperature higher than the
boiling point of water?

I'm attaching here one of the steps of the dynamic
Thank you in advance


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Received on Tue Oct 22 2013 - 09:00:03 PDT
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