Dear Amber users;
I'm concerned b/c I ran a GB + langevin dynamics simulation of a short
peptide (ACE GLY SER SER SER NME) and the average temperature (over
500,000 steps = 0.5 ns) is about 10 degrees above the target temperature.
I ran several
nanoseconds and for each 0.5 ns segment, the temperature is consistently
high. Below is the sander input and the output. Any ideas??
&cntrl
imin = 0,
nmropt = 0,
ntx = 5, irest = 1,
ntpr = 1000, ntwx = 1000,
ntwr = 1000,
ntf = 2,
ntb = 0,
cut = 50,
igb = 5,
GAMMA_LN=2
nstlim = 500000,
t = 0.0, dt = 0.001,
temp0 = 300.0, tempi = 300.0,
ntt = 3, dtemp = 0.0,
ntc = 2, tol = 0.00001,
&end
the output is:
A V E R A G E S O V E R 500000 S T E P S
NSTEP = 500000 TIME(PS) = 600.000 TEMP(K) = 312.64 PRESS = 0.0
Etot = -21.5145 EKtot = 38.8303 EPtot = -60.3448
BOND = 9.8020 ANGLE = 21.9661 DIHED = 15.2651
1-4 NB = 8.4020 1-4 EEL = 215.9107 VDWAALS = -6.9835
EELEC = -271.6598 EGB = -53.0474 RESTRAINT = 0.0000
a few nanoseconds later...
A V E R A G E S O V E R 500000 S T E P S
NSTEP = 500000 TIME(PS) = 5100.000 TEMP(K) = 313.29 PRESS = 0.0
Etot = -22.0479 EKtot = 38.9102 EPtot = -60.9581
BOND = 9.7891 ANGLE = 21.8143 DIHED = 15.0156
1-4 NB = 8.2395 1-4 EEL = 218.7032 VDWAALS = -6.5987
EELEC = -275.5212 EGB = -52.3999 RESTRAINT = 0.0000
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Received on Fri Sep 10 2004 - 13:25:59 PDT
