Alıntı accuratefreeenergy.gmail.com:
> Hi Umut,
>
> Could you try to use barostat=2 (MC barostat)? The current GPU/TI
> code might have some problems w/ barostat=1.
>
> If you still have problems, could you give us your input files so
> that we can take a look?
>
> Taisung
>
> -----Original Message-----
> From: Umut Çağan Uçar <ucaru.itu.edu.tr>
> Sent: Thursday, February 25, 2021 8:36 AM
> To: amber.ambermd.org
> Subject: [AMBER] GPU TI PROBLEM
>
>
> 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
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
Dear Taisung,
Thank you so much for your help. After a short equilibration and
production run with lambda 0.88729, I did not encounter the problem.
As far as I see, the main difference between the two barostats is that
MC does not calculate virial equation. In the output file, there are a
couple of warnings/knowledge such as:
"MC Barostat: Decreasing size of volume moves" and,
"MC Barostat: 5000 volume changes attempted.
| MC Barostat: 1372 changes successful ( 27.44%)"
I have never used MC barostat; thus, I assume these warnings/info are
inherent to the MC. Are these warnings normal?
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Received on Fri Feb 26 2021 - 01:00:03 PST
