Dear list,
We are studying protein phosphorylation (30 amino acids) structures with MD
simulations. We carried out simulations under the NPT ensemble with AMBER
12 PMEMD, cuda version. The temperature vs time plot shows that the
temperature fluctuates about 6 degrees plus/minus the initial temperature
which is 310K.
Is the 5 degrees fluctuation a kind of reasonable range in the NPT
ensemble?
Here is the input file:
Title
&cntrl
irest=1,ntx=5,
nstlim=5000000,dt=0.002,
temp0=310.0,ntt=1,tautp=1.0,
ntc=2,ntf=2,
cut=10.0,
ntpr=5000,ntwx=5000,ntwv=0,ntwe=0,
ntb=2,ntp=1,pres0=1.0,taup=1.0,
ipol=0,igb=0,
ntr=0,
iwrap=1,
&end
Waiting for your inputs,
Cheers,
Neha
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Received on Mon Mar 04 2013 - 07:00:02 PST
