Dear Amber users,
when I ran the 1st stage of heating simulation from 0 to 100K,
the ultimate temperature didn't surpass 12K.
Here are the last steps from output file:
NSTEP = 19950 TIME(PS) = 9.975 TEMP(K) = 11.36 PRESS =
0.0
Etot = -8576.1998 EKtot = 92.4017 EPtot =
-8668.6016
BOND = 134.2874 ANGLE = 457.9412 DIHED =
2215.2082
1-4 NB = 655.3423 1-4 EEL = 7913.8875 VDWAALS =
-1791.1388
EELEC = -14827.7755 EGB = -3426.3539 RESTRAINT =
0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by 0.040870 0.441520 0.052998
NSTEP = 20000 TIME(PS) = 10.000 TEMP(K) = 11.43 PRESS =
0.0
Etot = -8575.9895 EKtot = 93.0162 EPtot =
-8669.0057
BOND = 134.8024 ANGLE = 462.2500 DIHED =
2215.2976
1-4 NB = 649.7273 1-4 EEL = 7919.3754 VDWAALS =
-1791.1755
EELEC = -14836.4375 EGB = -3422.8453 RESTRAINT =
0.0000
------------------------------------------------------------------------------
A V E R A G E S O V E R 20000 S T E P S
NSTEP = 20000 TIME(PS) = 10.000 TEMP(K) = 6.77 PRESS =
0.0
Etot = -8649.1636 EKtot = 55.1012 EPtot =
-8704.2648
BOND = 126.2944 ANGLE = 439.5599 DIHED =
2217.1735
1-4 NB = 648.2991 1-4 EEL = 7915.4244 VDWAALS =
-1792.9242
EELEC = -14941.3298 EGB = -3316.7621 RESTRAINT =
0.0000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 20000 TIME(PS) = 10.000 TEMP(K) = 3.11 PRESS =
0.0
Etot = 43.9817 EKtot = 25.2987 EPtot =
19.1895
BOND = 5.4996 ANGLE = 13.4675 DIHED =
4.0147
1-4 NB = 2.0976 1-4 EEL = 6.1379 VDWAALS =
4.2862
EELEC = 72.7734 EGB = 71.7080 RESTRAINT =
0.0000
------------------------------------------------------------------------------
and the input file was:
Stage 1 heating of Endonuc 0 to 100K
&cntrl
imin=0, irest=0, ntx=1,
nstlim=20000, dt=0.0005,
ntc=2, ntf=2,
ntt=3, ig=-1,gamma_ln=0.01,
tautp=1.0,
tempi=0.0, temp0=100.0,
ntpr=50, ntwx=50,
ntb=0, igb=1,
cut=999.,rgbmax=999.
/
The molecule is a protein, 200 aa long.
Could you please explain me why the desired temperature hasn't been reached?
Kind regards,
Nick
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Received on Tue Nov 01 2016 - 11:00:02 PDT
