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 - 14:00:02 PDT
