Hi
First, beware that no one has really tested TPS with constant pH in
amber, so there might be surprises all around.
What happens if you try TPS at constant protonation ? Or even if you do
constant pH TPS at pH=-10 or +10, which effectively keeps protonation
constant ?
Also: if you look at your output, your bond and angles energies are HUGE.
This means yous system more or less blew up somewhere.
You should look at the dynamics file and try to find some bonds that
clearly extended a LOT during your MD, and start debugging backwards
from there.
Adrian
On 10/20/22 2:14 PM, Divya Rai via AMBER wrote:
> [External Email]
>
> Hello all!
>
> I am trying to carry out transition path sampling followed by umbrella
> sampling carried out on my system under constant pH conditions in explicit
> solvent. However, while doing so, the temperature is abruptly rising to as
> high as 8000 K. I am unable to understand the reason behind it. I am
> pasting my TPS input and a part of the corresponding output file as follows:
>
> *TPS.in:*
> &cntrl
> imin=0,
> iwrap=1,
> nstlim=200000,
> dt=0.001,
> temp0=300.0,
> ntpr=500,
> ntwx=500,
> cut=10.0,
> ntb=1,
> ntp=0,
> ntt=3,
> gamma_ln=2.0,
> icnstph=2,
> solvph=5.0,
> ntcnstph=500,
> ntrelax=200,
> saltcon=0.1,
> &end
>
> *TPS_pos.out:*
>
> NSTEP = 12500 TIME(PS) = 12.500 TEMP(K) = 7128.23 PRESS =
> 0.0
> Etot = 1562145.0541 EKtot = 996221.3512 EPtot =
> 565923.7029
> BOND = 461042.3731 ANGLE = 149054.0719 DIHED =
> 13537.7055
> 1-4 NB = 36450.3976 1-4 EEL = 1882.5654 VDWAALS =
> 62810.6024
> EELEC = -158854.0129 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.3077E-03
> ------------------------------------------------------------------------------
>
>
> NSTEP = 13000 TIME(PS) = 13.000 TEMP(K) = 6982.39 PRESS =
> 0.0
> Etot = 1646012.8371 EKtot = 975838.9304 EPtot =
> 670173.9067
> BOND = 457877.4767 ANGLE = 152164.5629 DIHED =
> 13657.7663
> 1-4 NB = 135897.2419 1-4 EEL = 3062.1700 VDWAALS =
> 65686.2771
> EELEC = -158171.5882 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.7148E-03
> ------------------------------------------------------------------------------
>
>
> NSTEP = 13500 TIME(PS) = 13.500 TEMP(K) = 6916.09 PRESS =
> 0.0
> Etot = 1528866.7826 EKtot = 966573.9452 EPtot =
> 562292.8375
> BOND = 450317.1076 ANGLE = 148701.8056 DIHED =
> 13750.3527
> 1-4 NB = 38113.2479 1-4 EEL = 2952.8831 VDWAALS =
> 66579.0707
> EELEC = -158121.6301 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.2925E-03
> ------------------------------------------------------------------------------
>
>
> NSTEP = 14000 TIME(PS) = 14.000 TEMP(K) = 7253.14 PRESS =
> 0.0
> Etot = 1625878.5058 EKtot = 1013678.8487 EPtot =
> 612199.6572
> BOND = 502799.3873 ANGLE = 150843.0712 DIHED =
> 13984.5422
> 1-4 NB = 30144.8702 1-4 EEL = 2884.4517 VDWAALS =
> 68977.0848
> EELEC = -157433.7502 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.5040E-03
> ------------------------------------------------------------------------------
>
>
> NSTEP = 14500 TIME(PS) = 14.500 TEMP(K) = 6771.02 PRESS =
> 0.0
> Etot = 1504379.1998 EKtot = 946299.3185 EPtot =
> 558079.8813
> BOND = 449003.3019 ANGLE = 149925.4241 DIHED =
> 13758.9701
> 1-4 NB = 33921.6670 1-4 EEL = 3605.0275 VDWAALS =
> 66160.3295
> EELEC = -158294.8388 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.7995E-03
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 14978; vmax = 22.5046
> vlimit exceeded for step 14982; vmax = 20.0489
> vlimit exceeded for step 14983; vmax = 25.1951
> vlimit exceeded for step 14984; vmax = 21.7514
> vlimit exceeded for step 14989; vmax = 20.7790
> vlimit exceeded for step 14990; vmax = 20.4740
> vlimit exceeded for step 14991; vmax = 20.1243
> vlimit exceeded for step 10; vmax = 25.2084
> vlimit exceeded for step 11; vmax = 22.0600
>
> NSTEP = 15000 TIME(PS) = 15.000 TEMP(K) = 7026.49 PRESS =
> 0.0
> Etot = 2139170.6204 EKtot = 982002.8767 EPtot =
> 1157167.7437
> BOND = 476022.4268 ANGLE = 150283.0606 DIHED =
> 14139.0281
> 1-4 NB = 22074.1524 1-4 EEL = 2666.1653 VDWAALS =
> 650093.5734
> EELEC = -158110.6629 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.5989E-03
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--
Dr. Adrian E. Roitberg (he/him/el)
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Oct 20 2022 - 12:00:03 PDT
