Dear AMBER Users and Developers,
I performed TI simulations on AMBER20 with GPU in order to calculate
pKa of aspartate residues. The problem I encountered is that the
protein undergoes denaturation immediately when I carry out gpu
implemented TI, which was seen in different initial structures and
protonation states as well. However, on both AMBER16 and AMBER20 cpu,
there was no such a problem when I gave the same initial structure and
parameters. I have followed the online tutorial(and the reference
paper) and performed several successful TI on cpu thus far. After
minimization, I equilibrated each system for 5ns with clambda=0. Then,
the same equilibrated structure was given to production runs with
lambda values 0.1127, 0.5, and 0.88729. I use Langevin thermostat to
control temperature at 300 K and I don't use softcore potential.
During denaturation, there was no temperature increase due to
instability. As given in the AMBER20 manual, there are some gti
specific parameters but I took the default values. I also tried
gti_add_sc=0 ,but the sample problem was still observed. Moreover, I
ran trial simulations for 4-5 steps by turning off the Langevin by
setting ntt=1 and write energy values for each step to see how
energies fluctuate comparing AMBER20 cpu with AMBER20 gpu TI in the
absence of random number from Langevin dynamics. According to the
results, there was no significant difference between gpu and cpu. By
the way, standard md simulations run without any problem on the same
gpus. Am I missing something for the gpu case? What am I supposed to
add or change for the gpu implented TI? Any help/suggestion will be
greatly appreciated!
The input file for clambda=0.88729 alongside the output files for the
first 4 steps of amber20 gpu and cpu without Langevin are as follows:
INPUT FILE FOR LAMBDA = 0.88729
&cntrl
imin = 0, nstlim = 2500000, cut = 9, dt = 0.002,
ntt = 3, tempi = 10, temp0 = 300.0, gamma_ln = 5, ig = -1,
ntp = 1,
ntb = 2, ntxo = 2, ioutfm = 1,
ntc = 2, ntf = 2,
ntwe = 2500, ntwx = 2500, ntpr = 2500, ntave = 2500,
icfe = 1, clambda = 0.88729,
timask1 = ':194', timask2 = ':389',
irest = 1, ntx = 5,
&end
&ewald
nfft1 = 96, nfft2 = 96, nfft3 = 96,
&end
GPU OUTPUT WITHOUT LANGEVIN
| TI region 1
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 300.70 PRESS = -58.7
Etot = -123867.3438 EKtot = 31621.7229 EPtot = -155489.0667
BOND = 1120.8117 ANGLE = 2959.9344 DIHED = 4105.9721
1-4 NB = 1367.5945 1-4 EEL = 17289.6476 VDWAALS = 18171.8734
EELEC = -200504.9004 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13490.6621 VIRIAL = 14139.0861 VOLUME = 511871.3360
Density =
1.0241
DV/DL = 66.6480
------------------------------------------------------------------------------
| TI region 2
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 300.70 PRESS = -58.7
Etot = -123867.3438 EKtot = 31621.7229 EPtot = -155489.0667
BOND = 1120.8117 ANGLE = 2959.9344 DIHED = 4105.9721
1-4 NB = 1367.5945 1-4 EEL = 17289.6476 VDWAALS = 18171.8734
EELEC = -200504.9004 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13490.6621 VIRIAL = 14139.0861 VOLUME = 511871.3360
Density =
1.0241
DV/DL = 66.6480
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
A V E R A G E S O V E R 1 S T E P S
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 300.70 PRESS = -58.7
Etot = -123867.3438 EKtot = 31621.7229 EPtot = -155489.0667
BOND = 1120.8117 ANGLE = 2959.9344 DIHED = 4105.9721
1-4 NB = 1367.5945 1-4 EEL = 17289.6476 VDWAALS = 18171.8734
EELEC = -200504.9004 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13490.6621 VIRIAL = 14139.0861 VOLUME = 511871.3360
Density =
1.0241
DV/DL = 66.6480
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000
Density =
0.0000
------------------------------------------------------------------------------
| TI region 2
A V E R A G E S O V E R 1 S T E P S
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 300.70 PRESS = -58.7
Etot = -123867.3438 EKtot = 31621.7229 EPtot = -155489.0667
BOND = 1120.8117 ANGLE = 2959.9344 DIHED = 4105.9721
1-4 NB = 1367.5945 1-4 EEL = 17289.6476 VDWAALS = 18171.8734
EELEC = -200504.9004 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13490.6621 VIRIAL = 14139.0861 VOLUME = 511871.3360
Density =
1.0241
DV/DL = 66.6480
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000
Density =
0.0000
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 1 STEPS
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 66.6480
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 13.2123 VDWAALS = 0.0000
EELEC = 53.4356 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000
Density =
0.0000
DV/DL = 66.6480
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 300.07 PRESS = -44.2
Etot = -123864.6384 EKtot = 31554.7891 EPtot = -155419.4275
BOND = 1105.4682 ANGLE = 2985.2113 DIHED = 4107.8366
1-4 NB = 1367.2018 1-4 EEL = 17291.2742 VDWAALS = 18175.0968
EELEC = -200451.5164 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13485.6504 VIRIAL = 13974.3132 VOLUME = 511868.6115
Density =
1.0241
DV/DL = 64.1542
------------------------------------------------------------------------------
| TI region 2
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 300.07 PRESS = -44.2
Etot = -123864.6384 EKtot = 31554.7891 EPtot = -155419.4275
BOND = 1105.4682 ANGLE = 2985.2113 DIHED = 4107.8366
1-4 NB = 1367.2018 1-4 EEL = 17291.2742 VDWAALS = 18175.0968
EELEC = -200451.5164 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13485.6504 VIRIAL = 13974.3132 VOLUME = 511868.6115
Density =
1.0241
DV/DL = 64.1542
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
A V E R A G E S O V E R 1 S T E P S
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 300.07 PRESS = -44.2
Etot = -123864.6384 EKtot = 31554.7891 EPtot = -155419.4275
BOND = 1105.4682 ANGLE = 2985.2113 DIHED = 4107.8366
1-4 NB = 1367.2018 1-4 EEL = 17291.2742 VDWAALS = 18175.0968
EELEC = -200451.5164 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13485.6504 VIRIAL = 13974.3132 VOLUME = 511868.6115
Density =
1.0241
DV/DL = 64.1542
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0014 EKtot = 0.0000 EPtot = 0.0020
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0002
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0003 VIRIAL = 0.0002 VOLUME = 0.0000
Density =
0.0000
DV/DL = 0.0000
------------------------------------------------------------------------------
| TI region 2
A V E R A G E S O V E R 1 S T E P S
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 300.07 PRESS = -44.2
Etot = -123864.6384 EKtot = 31554.7891 EPtot = -155419.4275
BOND = 1105.4682 ANGLE = 2985.2113 DIHED = 4107.8366
1-4 NB = 1367.2018 1-4 EEL = 17291.2742 VDWAALS = 18175.0968
EELEC = -200451.5164 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13485.6504 VIRIAL = 13974.3132 VOLUME = 511868.6115
Density =
1.0241
DV/DL = 64.1542
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0014 EKtot = 0.0000 EPtot = 0.0020
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0002
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0003 VIRIAL = 0.0002 VOLUME = 0.0000
Density =
0.0000
DV/DL = 0.0000
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 1 STEPS
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 64.1542
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 13.4762 VDWAALS = 0.0000
EELEC = 50.6780 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000
Density =
0.0000
DV/DL = 64.1542
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 299.69 PRESS = -26.8
Etot = -123864.8224 EKtot = 31515.1209 EPtot = -155379.9434
BOND = 1096.4784 ANGLE = 2971.9188 DIHED = 4108.0978
1-4 NB = 1366.3827 1-4 EEL = 17295.7003 VDWAALS = 18177.8843
EELEC = -200396.4056 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13481.0575 VIRIAL = 13777.1270 VOLUME = 511866.5470
Density =
1.0241
DV/DL = 60.4146
------------------------------------------------------------------------------
| TI region 2
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 299.69 PRESS = -26.8
Etot = -123864.8224 EKtot = 31515.1209 EPtot = -155379.9434
BOND = 1096.4784 ANGLE = 2971.9188 DIHED = 4108.0978
1-4 NB = 1366.3827 1-4 EEL = 17295.7003 VDWAALS = 18177.8843
EELEC = -200396.4056 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13481.0575 VIRIAL = 13777.1270 VOLUME = 511866.5470
Density =
1.0241
DV/DL = 60.4146
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
A V E R A G E S O V E R 1 S T E P S
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 299.69 PRESS = -26.8
Etot = -123864.8224 EKtot = 31515.1209 EPtot = -155379.9434
BOND = 1096.4784 ANGLE = 2971.9188 DIHED = 4108.0978
1-4 NB = 1366.3827 1-4 EEL = 17295.7003 VDWAALS = 18177.8843
EELEC = -200396.4056 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13481.0575 VIRIAL = 13777.1270 VOLUME = 511866.5470
Density =
1.0241
DV/DL = 60.4146
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0034
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0001
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0003 VOLUME = 0.0000
Density =
0.0000
------------------------------------------------------------------------------
| TI region 2
A V E R A G E S O V E R 1 S T E P S
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 299.69 PRESS = -26.8
Etot = -123864.8224 EKtot = 31515.1209 EPtot = -155379.9434
BOND = 1096.4784 ANGLE = 2971.9188 DIHED = 4108.0978
1-4 NB = 1366.3827 1-4 EEL = 17295.7003 VDWAALS = 18177.8843
EELEC = -200396.4056 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13481.0575 VIRIAL = 13777.1270 VOLUME = 511866.5470
Density =
1.0241
DV/DL = 60.4146
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0034
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0001
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0003 VOLUME = 0.0000
Density =
0.0000
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 1 STEPS
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 60.4146
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 13.6577 VDWAALS = 0.0000
EELEC = 46.7569 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000
Density =
0.0000
DV/DL = 60.4146
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 299.59 PRESS = -8.7
Etot = -123866.1946 EKtot = 31504.2721 EPtot = -155370.4667
BOND = 1100.7122 ANGLE = 2930.5149 DIHED = 4108.2955
1-4 NB = 1365.9913 1-4 EEL = 17302.5867 VDWAALS = 18178.3314
EELEC = -200356.8986 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13477.3201 VIRIAL = 13573.9122 VOLUME = 511865.2782
Density =
1.0241
DV/DL = 55.9308
------------------------------------------------------------------------------
| TI region 2
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 299.59 PRESS = -8.7
Etot = -123866.1946 EKtot = 31504.2721 EPtot = -155370.4667
BOND = 1100.7122 ANGLE = 2930.5149 DIHED = 4108.2955
1-4 NB = 1365.9913 1-4 EEL = 17302.5867 VDWAALS = 18178.3314
EELEC = -200356.8986 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13477.3201 VIRIAL = 13573.9122 VOLUME = 511865.2782
Density =
1.0241
DV/DL = 55.9308
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
A V E R A G E S O V E R 1 S T E P S
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 299.59 PRESS = -8.7
Etot = -123866.1946 EKtot = 31504.2721 EPtot = -155370.4667
BOND = 1100.7122 ANGLE = 2930.5149 DIHED = 4108.2955
1-4 NB = 1365.9913 1-4 EEL = 17302.5867 VDWAALS = 18178.3314
EELEC = -200356.8986 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13477.3201 VIRIAL = 13573.9122 VOLUME = 511865.2782
Density =
1.0241
DV/DL = 55.9308
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0003 EPtot = 0.0028
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0006 VDWAALS = 0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0003 VIRIAL = 0.0000 VOLUME = 0.0000
Density =
0.0000
------------------------------------------------------------------------------
| TI region 2
A V E R A G E S O V E R 1 S T E P S
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 299.59 PRESS = -8.7
Etot = -123866.1946 EKtot = 31504.2721 EPtot = -155370.4667
BOND = 1100.7122 ANGLE = 2930.5149 DIHED = 4108.2955
1-4 NB = 1365.9913 1-4 EEL = 17302.5867 VDWAALS = 18178.3314
EELEC = -200356.8986 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13477.3201 VIRIAL = 13573.9122 VOLUME = 511865.2782
Density =
1.0241
DV/DL = 55.9308
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0003 EPtot = 0.0028
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0006 VDWAALS = 0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0003 VIRIAL = 0.0000 VOLUME = 0.0000
Density =
0.0000
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 1 STEPS
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 55.9308
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 13.7307 VDWAALS = 0.0000
EELEC = 42.2001 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 0.0000
Density =
0.0000
DV/DL = 55.9308
------------------------------------------------------------------------------
|===============================================================================
CPU OUTPUT WITHOUT LANGEVIN
| TI region 1
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 300.71 PRESS
= -58.6
Etot = -123867.1727 EKtot = 31622.0339 EPtot =
-155489.2066
BOND = 1120.8117 ANGLE = 2959.9344 DIHED =
4105.9713
1-4 NB = 1367.5947 1-4 EEL = 17289.6474 VDWAALS =
18171.9043
EELEC = -200505.0704 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13490.7172 VIRIAL = 14138.6335 VOLUME =
511871.3360
Density =
1.0241
DV/DL = 66.6479
Ewald error estimate: 0.8521E-06
------------------------------------------------------------------------------
| TI region 2
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 300.71 PRESS
= -58.6
Etot = -123867.1727 EKtot = 31622.0339 EPtot =
-155489.2066
BOND = 1120.8117 ANGLE = 2959.9344 DIHED =
4105.9713
1-4 NB = 1367.5947 1-4 EEL = 17289.6474 VDWAALS =
18171.9043
EELEC = -200505.0704 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13490.7172 VIRIAL = 14138.6335 VOLUME =
511871.3360
Density =
1.0241
DV/DL = 66.6479
Ewald error estimate: 0.8521E-06
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
A V E R A G E S O V E R 1 S T E P S
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 300.71 PRESS
= -58.6
Etot = -123867.1727 EKtot = 31622.0339 EPtot =
-155489.2066
BOND = 1120.8117 ANGLE = 2959.9344 DIHED =
4105.9713
1-4 NB = 1367.5947 1-4 EEL = 17289.6474 VDWAALS =
18171.9043
EELEC = -200505.0704 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13490.7172 VIRIAL = 14138.6335 VOLUME =
511871.3360
Density =
1.0241
DV/DL = 66.6479
Ewald error estimate: 0.8521E-06
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
| TI region 2
A V E R A G E S O V E R 1 S T E P S
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 300.71 PRESS
= -58.6
Etot = -123867.1727 EKtot = 31622.0339 EPtot =
-155489.2066
BOND = 1120.8117 ANGLE = 2959.9344 DIHED =
4105.9713
1-4 NB = 1367.5947 1-4 EEL = 17289.6474 VDWAALS =
18171.9043
EELEC = -200505.0704 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13490.7172 VIRIAL = 14138.6335 VOLUME =
511871.3360
Density =
1.0241
DV/DL = 66.6479
Ewald error estimate: 0.8521E-06
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 1 STEPS
NSTEP = 1 TIME(PS) = 5000.002 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
66.6479
BOND = -0.0000 ANGLE = -0.0000 DIHED =
-0.0000
1-4 NB = 0.0000 1-4 EEL = 13.2123 VDWAALS =
0.0000
EELEC = 53.4356 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
DV/DL = 66.6479
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 300.07 PRESS
= -44.2
Etot = -123864.0417 EKtot = 31555.3485 EPtot =
-155419.3902
BOND = 1105.6521 ANGLE = 2985.4905 DIHED =
4107.8158
1-4 NB = 1367.1841 1-4 EEL = 17291.2674 VDWAALS =
18175.0731
EELEC = -200451.8733 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13485.7317 VIRIAL = 13974.0037 VOLUME =
511868.6136
Density =
1.0241
DV/DL = 64.0057
Ewald error estimate: 0.6810E-05
------------------------------------------------------------------------------
| TI region 2
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 300.07 PRESS
= -44.2
Etot = -123864.0417 EKtot = 31555.3485 EPtot =
-155419.3902
BOND = 1105.6521 ANGLE = 2985.4905 DIHED =
4107.8158
1-4 NB = 1367.1841 1-4 EEL = 17291.2674 VDWAALS =
18175.0731
EELEC = -200451.8733 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13485.7317 VIRIAL = 13974.0037 VOLUME =
511868.6136
Density =
1.0241
DV/DL = 64.0057
Ewald error estimate: 0.6810E-05
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
A V E R A G E S O V E R 1 S T E P S
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 300.07 PRESS
= -44.2
Etot = -123864.0417 EKtot = 31555.3485 EPtot =
-155419.3902
BOND = 1105.6521 ANGLE = 2985.4905 DIHED =
4107.8158
1-4 NB = 1367.1841 1-4 EEL = 17291.2674 VDWAALS =
18175.0731
EELEC = -200451.8733 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13485.7317 VIRIAL = 13974.0037 VOLUME =
511868.6136
Density =
1.0241
DV/DL = 64.0057
Ewald error estimate: 0.6810E-05
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0002 VIRIAL = 0.0000 VOLUME =
0.0078
Density =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
| TI region 2
A V E R A G E S O V E R 1 S T E P S
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 300.07 PRESS
= -44.2
Etot = -123864.0417 EKtot = 31555.3485 EPtot =
-155419.3902
BOND = 1105.6521 ANGLE = 2985.4905 DIHED =
4107.8158
1-4 NB = 1367.1841 1-4 EEL = 17291.2674 VDWAALS =
18175.0731
EELEC = -200451.8733 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13485.7317 VIRIAL = 13974.0037 VOLUME =
511868.6136
Density =
1.0241
DV/DL = 64.0057
Ewald error estimate: 0.6810E-05
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0002 VIRIAL = 0.0000 VOLUME =
0.0078
Density =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 1 STEPS
NSTEP = 2 TIME(PS) = 5000.004 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
64.0057
BOND = 0.0000 ANGLE = 0.0000 DIHED =
-0.0000
1-4 NB = -0.0000 1-4 EEL = 13.4849 VDWAALS =
-0.0000
EELEC = 50.5208 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
DV/DL = 64.0057
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 299.69 PRESS
= -26.8
Etot = -123864.2771 EKtot = 31515.2813 EPtot =
-155379.5584
BOND = 1096.9471 ANGLE = 2972.7754 DIHED =
4108.0121
1-4 NB = 1366.3378 1-4 EEL = 17295.6781 VDWAALS =
18177.7897
EELEC = -200397.0986 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13481.1354 VIRIAL = 13776.9529 VOLUME =
511866.5508
Density =
1.0241
DV/DL = 60.0123
Ewald error estimate: 0.1390E-04
------------------------------------------------------------------------------
| TI region 2
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 299.69 PRESS
= -26.8
Etot = -123864.2771 EKtot = 31515.2813 EPtot =
-155379.5584
BOND = 1096.9471 ANGLE = 2972.7754 DIHED =
4108.0121
1-4 NB = 1366.3378 1-4 EEL = 17295.6781 VDWAALS =
18177.7897
EELEC = -200397.0986 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13481.1354 VIRIAL = 13776.9529 VOLUME =
511866.5508
Density =
1.0241
DV/DL = 60.0123
Ewald error estimate: 0.1390E-04
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
A V E R A G E S O V E R 1 S T E P S
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 299.69 PRESS
= -26.8
Etot = -123864.2771 EKtot = 31515.2813 EPtot =
-155379.5584
BOND = 1096.9471 ANGLE = 2972.7754 DIHED =
4108.0121
1-4 NB = 1366.3378 1-4 EEL = 17295.6781 VDWAALS =
18177.7897
EELEC = -200397.0986 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13481.1354 VIRIAL = 13776.9529 VOLUME =
511866.5508
Density =
1.0241
DV/DL = 60.0123
Ewald error estimate: 0.1390E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0002
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
| TI region 2
A V E R A G E S O V E R 1 S T E P S
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 299.69 PRESS
= -26.8
Etot = -123864.2771 EKtot = 31515.2813 EPtot =
-155379.5584
BOND = 1096.9471 ANGLE = 2972.7754 DIHED =
4108.0121
1-4 NB = 1366.3378 1-4 EEL = 17295.6781 VDWAALS =
18177.7897
EELEC = -200397.0986 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13481.1354 VIRIAL = 13776.9529 VOLUME =
511866.5508
Density =
1.0241
DV/DL = 60.0123
Ewald error estimate: 0.1390E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0002
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 1 STEPS
NSTEP = 3 TIME(PS) = 5000.006 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
60.0123
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = -0.0000 1-4 EEL = 13.6852 VDWAALS =
-0.0000
EELEC = 46.3271 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
DV/DL = 60.0123
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 299.59 PRESS
= -8.7
Etot = -123866.1251 EKtot = 31504.1736 EPtot =
-155370.2987
BOND = 1101.1670 ANGLE = 2931.7899 DIHED =
4108.1013
1-4 NB = 1365.9103 1-4 EEL = 17302.5322 VDWAALS =
18178.1368
EELEC = -200357.9363 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13477.3805 VIRIAL = 13573.8955 VOLUME =
511865.2830
Density =
1.0241
DV/DL = 55.2192
Ewald error estimate: 0.2958E-04
------------------------------------------------------------------------------
| TI region 2
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 299.59 PRESS
= -8.7
Etot = -123866.1251 EKtot = 31504.1736 EPtot =
-155370.2987
BOND = 1101.1670 ANGLE = 2931.7899 DIHED =
4108.1013
1-4 NB = 1365.9103 1-4 EEL = 17302.5322 VDWAALS =
18178.1368
EELEC = -200357.9363 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13477.3805 VIRIAL = 13573.8955 VOLUME =
511865.2830
Density =
1.0241
DV/DL = 55.2192
Ewald error estimate: 0.2958E-04
------------------------------------------------------------------------------
|===============================================================================
| TI region 1
A V E R A G E S O V E R 1 S T E P S
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 299.59 PRESS
= -8.7
Etot = -123866.1251 EKtot = 31504.1736 EPtot =
-155370.2987
BOND = 1101.1670 ANGLE = 2931.7899 DIHED =
4108.1013
1-4 NB = 1365.9103 1-4 EEL = 17302.5322 VDWAALS =
18178.1368
EELEC = -200357.9363 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13477.3805 VIRIAL = 13573.8955 VOLUME =
511865.2830
Density =
1.0241
DV/DL = 55.2192
Ewald error estimate: 0.2958E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0001
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0048 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0002 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
| TI region 2
A V E R A G E S O V E R 1 S T E P S
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 299.59 PRESS
= -8.7
Etot = -123866.1251 EKtot = 31504.1736 EPtot =
-155370.2987
BOND = 1101.1670 ANGLE = 2931.7899 DIHED =
4108.1013
1-4 NB = 1365.9103 1-4 EEL = 17302.5322 VDWAALS =
18178.1368
EELEC = -200357.9363 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 13477.3805 VIRIAL = 13573.8955 VOLUME =
511865.2830
Density =
1.0241
DV/DL = 55.2192
Ewald error estimate: 0.2958E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0001
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
EELEC = 0.0048 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0002 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 1 STEPS
NSTEP = 4 TIME(PS) = 5000.008 TEMP(K) = 0.00 PRESS
= 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
55.2192
BOND = 0.0000 ANGLE = -0.0000 DIHED =
-0.0000
1-4 NB = 0.0000 1-4 EEL = 13.7861 VDWAALS =
0.0000
EELEC = 41.4331 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
DV/DL = 55.2192
Ewald error estimate: 0.0000E+00
------------------------------------------------------------------------------
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Received on Thu Feb 25 2021 - 06:00:09 PST
