the pressure will fluctuate (it's not constant in an instantaneous sense),
but your density looks good so I think it's ok.
I don't think that's related to why it stops. did you get any error message
to another file, maybe something output from your queueing system?
On Fri, Apr 8, 2022 at 4:47 PM Artur Hermano <artur.hermano.hotmail.com>
wrote:
> Hello Amber team,
>
> I am trying to run a simulation that, after minimization goes through a
> NVT heating step and then through a NPT equilibration step. I am using the
> Berendsen barostat for the NPT step, but it seems not to be working.
> Despite the previous steps running fine, my equilibration stops all of a
> sudden with no error messages on the bottom of the equi.out file (see
> below). My equilibration input file is:
>
> Equi
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> nstlim=50000,
> dt=0.002,
> ntf=2,
> ntc=2,
> tempi=300.0,
> temp0=300.0,
> ntpr=500,
> ntwx=500,
> cut=10.0,
> ntb=2,
> pres0=1.0,
> ntp=1,
> taup=2.0,
> ntt=3,
> gamma_ln=1.0,
> /
>
> And these are the bottom lines of my equi.out file:
>
> NSTEP = 22500 TIME(PS) = 145.000 TEMP(K) = 300.69 PRESS =
> -80.5
> Etot = -106653.7224 EKtot = 27528.5859 EPtot =
> -134182.3083
> BOND = 1203.8180 ANGLE = 3190.8939 DIHED =
> 5012.8786
> 1-4 NB = 1420.7867 1-4 EEL = 13569.6107 VDWAALS =
> 14268.7934
> EELEC = -172849.0895 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 11546.7037 VIRIAL = 12320.0722 VOLUME =
> 444926.8592
> Density =
> 1.0244
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 23000 TIME(PS) = 146.000 TEMP(K) = 298.83 PRESS =
> 16.8
> Etot = -106989.9082 EKtot = 27357.8926 EPtot =
> -134347.8008
> BOND = 1195.2600 ANGLE = 3169.3732 DIHED =
> 5000.9721
> 1-4 NB = 1405.4871 1-4 EEL = 13560.7227 VDWAALS =
> 14215.4113
> EELEC = -172895.0271 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 11520.0326 VIRIAL = 11358.4814 VOLUME =
> 444598.2344
> Density =
> 1.0251
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 23500 TIME(PS) = 147.000 TEMP(K) = 296.37 PRESS =
> -3.2
> Etot = -107084.2024 EKtot = 27133.1016 EPtot =
> -134217.3040
> BOND = 1180.1769 ANGLE = 3129.3570 DIHED =
> 5012.9329
> 1-4 NB = 1429.4178 1-4 EEL = 13670.0174 VDWAALS =
> 14530.8318
> EELEC = -173170.0378 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 11581.9544 VIRIAL = 11612.9675 VOLUME =
> 444105.4865
> Density =
> 1.0263
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 24000 TIME(PS) = 148.000 TEMP(K) = 300.35 PRESS =
> -32.2
> Etot = -107062.9372 EKtot = 27496.6387 EPtot =
> -134559.5759
> BOND = 1142.9891 ANGLE = 3215.9534 DIHED =
> 4999.4223
> 1-4 NB = 1424.9494 1-4 EEL = 13680.1911 VDWAALS =
> 14481.5016
> EELEC = -173504.5828 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 11601.6809 VIRIAL = 11910.2262 VOLUME =
> 444245.4810
> Density =
> 1.0260
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 24500 TIME(PS) = 149.000 TEMP(K) = 297.84 PRESS =
> -72.4
> Etot = -107278.1062 EKtot = 27267.2070 EPtot =
> -134545.3133
> BOND = 1135.5286 ANGLE = 3195.0653 DIHED =
> 5006.3317
> 1-4 NB = 1414.9647 1-4 EEL = 13662.5592 VDWAALS =
> 14327.2018
> EELEC = -173286.9645 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 11442.0238 VIRIAL = 12135.9224 VOLUME =
> 443834.8519
> Density =
> 1.0269
>
> ------------------------------------------------------------------------------
>
> As you can see, the pressure is clearly far from constant, but I don't
> think it should... Am I missing something here? Any help is very much
> appreciated!
>
> Thank you so much in advance!
>
> Artur
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Received on Fri Apr 08 2022 - 14:30:02 PDT
