Hi,
I do not follow the TI reflector threads, but here are some comments:
ensure that your amber14 is fully up to date with patches.
read the updates section of the amber web site to see if there are relevant patches.
try amber16.
If you cannot find evidence of and no one else replies indicating that
this is a known bug then send verbose and verbatim details:
in particular, I do not see the ^. character in your pasted text, so
please send the input and output decks as an attachment
as well as details regarding your installation - compiler, OS versions, etc.
scott
On Thu, Jul 21, 2016 at 05:52:53PM +0000, Khabiri, Morteza wrote:
>
> I am running fast growth TI calculation via amber14, pmemd. The lambda increasing via dynlmb option gradually. In a few cases I have got some wired line with (^.^.) symbol. In addition it seems the output is combing with some other outputs in a way that lambda value decreasing instead of increasing but after few steps it started to increasing from 0 to one.
> It would be helpful to let me know if you have any similar cases like this. The lines are pasted.
>
> runti
> &cntrl
> imin = 0, nstlim = 30000, irest = 1, ntx = 5, dt = 0.002,
> ntt = 3, temp0 = 298.0, gamma_ln = 5.0,nscm=0,
> ntc = 2, ntf = 1, ntb = 1, ntp = 0,
> ioutfm = 1, iwrap = 0, ntxo = 2,
> ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 1000,
>
> icfe = 1, clambda = 0.8000, idecomp=0,
> timask1 = ':14,39', timask2 = ':53,54', scalpha = 0.2, scbeta = 9.0,
> ifsc=1, logdvdl=1, dynlmb=0.0001, ntave=15,
> scmask1 = ':14,39', scmask2 = ':53,54'
> /
> &ewald
> /
>
> Ewald error estimate: 0.0000E+00
> ------------------------------------------------------------------------------
>
> |===============================================================================
>
> Dynamically changing lambda: Increased clambda by 0.0001 to 0.8509
>
> |===============================================================================
>
> | TI region 1
>
>
> A V E R A G E S O V E R 15 S T E P S
>
>
> NSTEP = 7650 TIME(PS) = 275.300 TEMP(K) = 297.85 PRESS = 0.0
> Etot = -661688.4134 EKtot = 141008.8464 EPtot = -802697.2598
> BOND = 510.4082 ANGLE = 987.3983 DIHED = 1424.5219
> 1-4 NB = 421.2330 1-4 EEL = -5336.6309 VDWAALS = 117236.0829
> EELEC = -917940.2731 EHBOND = 0.0000 RESTRAINT = 0.0000
> DV/DL = -70.6246
> Ewald error estimate: 0.1543E-03
> ------------------------------------------------------------------------------
>
> Softcore part of the system: 63 atoms, TEMP(K) = 304.26
> SC_Etot= -125.5638 SC_EKtot= 50.4866 SC_EPtot = -176.0504
> SC_BOND= 19.3961 SC_ANGLE= 32.0101 SC_DIHED = 69.5653
> SC_14NB= 19.6191 SC_14EEL= -373.0445 SC_VDW = -3.6519
> SC_EEL = 60.0555
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
> SC_EEL_DER= -103.9345 SC_VDW_DER= 29.2519 SC_DERIV = -74.6826
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 7650 TIME(PS) = 275.300 TEMP(K) = 0.19 PRESS = 0.0
> Etot = 72.6249 EKtot = 89.7880 EPtot = 97.7867
> BOND = 14.4724 ANGLE = 13.1604 DIHED = 7.0761
> 1-4 NB = 5.3980 1-4 EEL = 3.0384 VDWAALS = 85.4925
> EELEC = 134.8354 EHBOND = 0.0000 RESTRAINT = 0.0000
> DV/DL = 20.4474
> Ewald error estimate: 0.1637E-04
> ------------------------------------------------------------------------------
>
> Softcore part of the system: 63 atoms, TEMP(K) = 16.68
> SC_Etot= 10.3650 SC_EKtot= 2.7670 SC_EPtot = 9.6968
> SC_BOND= 1.7914 SC_ANGLE= 2.9810 SC_DIHED = 1.8774
> SC_14NB= 1.0688 SC_14EEL= 4.5169 SC_VDW = 0.7726
> SC_EEL = 10.4380
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
> SC_EEL_DER= 5.9250 SC_VDW_DER= 4.2259 SC_DERIV = 2.0467
> ------------------------------------------------------------------------------
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 7650 TIME(PS) = 275.300 TEMP(K) = 0.19 PRESS = 0.0
> Etot = 72.6249 EKtot = 89.7880 EPtot = 97.7867
> BOND = 14.4724 ANGLE = 13.1604 DIHED = 7.0761
> 1-4 NB = 5.3980 1-4 EEL = 3.0384 VDWAALS = 85.4925
> EELEC = 134.8354 EHBOND = 0.0000 RESTRAINT = 0.0000
> DV/DL = 20.4474
> Ewald error estimate: 0.1637E-04
> ------------------------------------------------------------------------------
>
> Softcore part of the system: 63 atoms, TEMP(K) = 16.68
> SC_Etot= 10.3650 SC_EKtot= 2.7670 SC_EPtot = 9.6968
> SC_BOND= 1.7914 SC_ANGLE= 2.9810 SC_DIHED = 1.8774
> SC_14NB= 1.0688 SC_14EEL= 4.5169 SC_VDW = 0.7726
> SC_EEL = 10.4380
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
> SC_EEL_DER= 5.9250 SC_VDW_DER= 4.2259 SC_DERIV = 2.0467
> ------------------------------------------------------------------------------
>
>
> | TI region 2
>
>
> A V E R A G E S O V E R 15 S T E P S
>
>
> NSTEP = 7650 TIME(PS) = 275.300 TEMP(K) = 297.86 PRESS = SC_RES_D Etot = -661685.3 SC_14NB= 18.3303 SC_14EEL= -24.8620 SC_VDW = -7.0892
> SC_EEL = -154.5765
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
> SC_EEL_DER= -72.2507 SC_VDW_DER= 13.9258 SC_DERIV = -58.3250
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 30 TIME(PS) = 260.060 TEMP(K) = 0.55 PRESS = 0.0
> Etot = 141.5940 EKtot = 260.7994 EPtot = 125.6889
> BOND = 10.2899 ANGLE = 25.9256 DIHED = 5.6068
> 1-4 NB = 1.2961 1-4 EEL = 15.8023 VDWAALS = 105.6176
> EELEC = 57.6005 EHBOND = 0.0000 RESTRAINT = 0.0000
> DV/DL = 27.8295
> Ewald error estimate: 0.3084E-04
> ------------------------------------------------------------------------------
> ------------------------------------------------------------------------------
>
> Softcore part of the system: 64 atoms, TEMP(K) = 13.52
> SC_Etot= 11.0560 SC_EKtot= 2.2695 SC_EPtot = 12.0172
> SC_BOND= 1.8150 SC_ANGLE= 1.3288 SC_DIHED = 0.5875
> SC_14NB= 1.2278 SC_14EEL= 3.0629 SC_VDW = 0.5237
> SC_EEL = 11.9598
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
> SC_EEL_DER= 1.4155 SC_VDW_DER= 1.1407 SC_DERIV = 0.8989
> ------------------------------------------------------------------------------
>
>
> DV/DL, AVERAGES OVER 15 STEPS
>
>
> NSTEP = 30 TIME(PS) = 260.060 TEMP(K) = 0.55 PRESS = 0.0
> Etot = 0.0000 EKtot = 0.0000 EPtot = -26.5558
> BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 4.8178
> EELEC = -31.3736 EHBOND = 0.0000 RESTRAINT = 0.0000
> DV/DL = -26.5558
> Ewald error estimate: 0.0000E+00
> ------------------------------------------------------------------------------
>
> |===============================================================================
>
> Dynamically changing lambda: Increased clambda by 0.0001 to 0.8002
>
> |===============================================================================
> | TI region 1
>
>
> A V E R A G E S O V E R 15 S T E P S
>
>
> NSTEP = 45 TIME(PS) = 260.090 TEMP(K) = 298.40 PRESS = 0.0
> Etot = -661051.1564 EKtot = 141267.8909 EPtot = -802319.0473
> BOND = 516.7320 ANGLE = 1005.0492 DIHED = 1419.9448
> 1-4 NB = 413.2974 1-4 EEL = -5344.2962 VDWAALS = 116463.5331
> EELEC = -916793.3076 EHBOND = 0.0000 RESTRAINT = 0.0000
> DV/DL = -61.5375
> Ewald error estimate: 0.1674E-03
> ------------------------------------------------------------------------------
>
> Softcore part of the system: 63 atoms, TEMP(K) = 320.89
> SC_Etot= -91.1596 SC_EKtot= 53.2447 SC_EPtot = -144.4043
> SC_BOND= 16.2298 SC_ANGLE= 32.7884 SC_DIHED = 72.8380
> SC_14NB= 19.5174 SC_14EEL= -374.0920 SC_VDW = -7.8836
> SC_EEL = 96.1976
> SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
> SC_EEL_DER= -73.9018 SC_VDW_DER= 16.8489 SC_DERIV = -57.0529
> ------------------------------------------------------------------------------
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Received on Fri Jul 22 2016 - 14:30:03 PDT
