Dear amber users,
I have a question regarding explicit solvent constant pH simulation of
protein. The problem is that mean temperature printed in output file is
well below requested temperature of 300 K. I assume that it has
something to do with solvent relaxation step during which the protein is
frozen.
The question is whether it is only a problem with temperature showed in
the output file, or is it a deeper problem of incorrect coupling with
the thermal bath. Can I just ignore this issue?
Here is fragment of output:
NSTEP = 11000 TIME(PS) = 4422.000 TEMP(K) = 275.67 PRESS
= 0.0
NSTEP = 12000 TIME(PS) = 4424.000 TEMP(K) = 276.72 PRESS
= 0.0
NSTEP = 13000 TIME(PS) = 4426.000 TEMP(K) = 272.92 PRESS
= 0.0
NSTEP = 14000 TIME(PS) = 4428.000 TEMP(K) = 299.79 PRESS
= 0.0
NSTEP = 15000 TIME(PS) = 4430.000 TEMP(K) = 274.19 PRESS
= 0.0
NSTEP = 16000 TIME(PS) = 4432.000 TEMP(K) = 301.80 PRESS
= 0.0
NSTEP = 17000 TIME(PS) = 4434.000 TEMP(K) = 274.60 PRESS
= 0.0
NSTEP = 18000 TIME(PS) = 4436.000 TEMP(K) = 276.55 PRESS
= 0.0
NSTEP = 19000 TIME(PS) = 4438.000 TEMP(K) = 298.17 PRESS
= 0.0
NSTEP = 20000 TIME(PS) = 4440.000 TEMP(K) = 275.76 PRESS
= 0.0
NSTEP = 21000 TIME(PS) = 4442.000 TEMP(K) = 274.77 PRESS
= 0.0
NSTEP = 22000 TIME(PS) = 4444.000 TEMP(K) = 300.32 PRESS
= 0.0
NSTEP = 23000 TIME(PS) = 4446.000 TEMP(K) = 276.98 PRESS
= 0.0
NSTEP = 24000 TIME(PS) = 4448.000 TEMP(K) = 298.93 PRESS
= 0.0
NSTEP = 25000 TIME(PS) = 4450.000 TEMP(K) = 274.52 PRESS
= 0.0
NSTEP = 26000 TIME(PS) = 4452.000 TEMP(K) = 274.62 PRESS
= 0.0
NSTEP = 27000 TIME(PS) = 4454.000 TEMP(K) = 274.36 PRESS
= 0.0
NSTEP = 28000 TIME(PS) = 4456.000 TEMP(K) = 299.36 PRESS
= 0.0
NSTEP = 29000 TIME(PS) = 4458.000 TEMP(K) = 274.12 PRESS
= 0.0
NSTEP = 30000 TIME(PS) = 4460.000 TEMP(K) = 277.08 PRESS
= 0.0
NSTEP = 31000 TIME(PS) = 4462.000 TEMP(K) = 276.03 PRESS
= 0.0
NSTEP = 32000 TIME(PS) = 4464.000 TEMP(K) = 276.08 PRESS
= 0.0
NSTEP = 33000 TIME(PS) = 4466.000 TEMP(K) = 276.44 PRESS
= 0.0
NSTEP = 34000 TIME(PS) = 4468.000 TEMP(K) = 299.66 PRESS
= 0.0
... and here is the input:
Explicit solvent constant pH MD
&cntrl
imin=0, irest=1, ntx=5, ntxo=2,
ntpr=1000, ntwx=1000, nstlim=5000000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=10, iwrap=1,
ioutfm=1, icnstph=2, ntcnstph=100,
solvph=6.6, ntrelax=100, saltcon=0.1,
/
Thanks in advance for your help.
--
*******************************************
Maciej S. Maciejczyk, PhD
Division of Physics and Biophysics
Faculty of Food Sciences
University of Warmia and Mazury in Olsztyn
ul. Oczapowskiego 4
10-719 Olsztyn
Poland
*******************************************
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Received on Thu Jan 11 2018 - 00:00:02 PST
