Dear Amber users,
after 500ns long accelerated MD run of a small protein (42aa, SPC/E water,
0.15M NaCl + 6Cl-,
15A box) the average density dropped to 0.9943. Although it's only slightly
lower than 1, it hardly corresponds to the physical reality. aMD simulation
followed the 15ns NPT run when density looked normal ( 1.0138 ).
The previuos steps were minimization, restraned NVT heating and NPT density
equillibration.
What could be the reason for density to decrease?
Here are the mdin and the end of aMD output files:
aMD_NPT
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
tautp = 10.0, ig=-1,
barostat=2,
cut = 9.0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln=1.0, nscm=5000,
nstlim = 250000000, dt = 0.002,
ntpr = 1000, ntwx = 1000, ntwr = 10000,
ioutfm=1, iwrap=1, iamd=3,
ethreshd=695, alphad=33.6,
ethreshp=-105278, alphap=4530,
/
**************************************************************
A V E R A G E S O V E R 250000 S T E P S
NSTEP =250000000 TIME(PS) = 518069.998 TEMP(K) = 300.01 PRESS =
0.0
Etot = -88497.0374 EKtot = 16999.8508 EPtot =
-105496.8883
BOND = 156.3031 ANGLE = 409.5914 DIHED =
680.2098
1-4 NB = 147.5610 1-4 EEL = 187.5102 VDWAALS =
17719.3268
EELEC = -124813.6640 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 16.2734
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
287595.3107
Density =
0.9943
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP =250000000 TIME(PS) = 518069.998 TEMP(K) = 1.79 PRESS =
0.0
Etot = 106.8858 EKtot = 101.2223 EPtot =
35.9813
BOND = 11.2999 ANGLE = 16.4056 DIHED =
5.5340
1-4 NB = 5.7567 1-4 EEL = 25.1555 VDWAALS =
167.9829
EELEC = 177.9544 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 4.7458
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
755.6965
Density =
0.0026
**********************************************************************************************
And also the mdin and statistics from the preceding NPT 15ns run:
15ns_NPT
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
tautp = 10.0, ig=-1,
barostat=2,
cut = 9.0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln=1.0, nscm=5000,
nstlim = 7500000, dt = 0.002,
ntpr = 10000, ntwx = 10000, ntwr = 25000,
ioutfm=1, iwrap=1,
/
***********************************************************************
A V E R A G E S O V E R 750 S T E P S
NSTEP = 7500000 TIME(PS) = 18070.000 TEMP(K) = 300.07 PRESS =
0.0
Etot = -92804.3367 EKtot = 17003.3156 EPtot =
-109807.6523
BOND = 146.1500 ANGLE = 386.7601 DIHED =
527.1965
1-4 NB = 148.0361 1-4 EEL = 143.2874 VDWAALS =
19238.2724
EELEC = -130397.3548 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
282076.7431
Density =
1.0138
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 7500000 TIME(PS) = 18070.000 TEMP(K) = 1.84 PRESS =
0.0
Etot = 195.1319 EKtot = 104.1916 EPtot =
161.5145
BOND = 10.1971 ANGLE = 15.2048 DIHED =
8.9386
1-4 NB = 5.1050 1-4 EEL = 21.3382 VDWAALS =
172.8649
EELEC = 275.2526 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
710.4472
Density =
0.0026
Thank you in advance,
Nick
Nikolay Kuzmich
Department of Drug Safety,
Research Institute of Influenza,
WHO National Influenza Centre of Russia,
15/17 Professor Popov St.,
Saint-Petersburg
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Received on Thu Aug 02 2018 - 07:30:01 PDT
