Dear Amber users
I'm facing a problem in a simulation of a protein in water (TIP3P) with counter ions and parallelepipedic periodic boundary conditions with polarization
The simulations worked all right for 15 ns : nice conservation of T and P low rmsd but the polarization energy and hence Epot and Etot steadily increase...
I must be missing some important option in the .in file
Here it is
CPT production run: 800 ps to reach 1 ns
&cntrl
nstlim=800000, dt=0.001,
! restart
irest=1, ntx=5,
ntpr=500, ntwr=5000, ntwx=5000,
tempi=300.0, temp0=300.0, pres0=1.0,
! ntt=3 Use Langevin dynamics with the collision frequency γ given by gamma_ln
ntt=3, gamma_ln = 1.0,
tautp=2.0,
! ntb=2 constant pressure
ntb=2,
! ntp Flag for constant pressure dynamics. ntp=1 md with isotropic position scaling
ntp=1,
! ntc Flag for SHAKE to perform bond length constraints. to employ TIP3P set NTF = NTC = 2
ntc=2, ntf=2,
! evaluate slowly-varying terms in the force field less frequently.
nrespa=1,
! no restraints
ntr=0,
ipol=1,
&end
Here for only 800 ps
Lines of output
NSTEP = 500 TIME(PS) = 200.500 TEMP(K) = 299.31 PRESS = 74.5
Etot = -74898.0013 EKtot = 9195.2868 EPtot = -84093.2881
BOND = 209.7914 ANGLE = 541.8550 DIHED = 791.7732
1-4 NB = 278.1858 1-4 EEL = 3222.7867 VDWAALS = 38592.0323
EELEC = -93496.7202 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 4227.8054 VIRIAL = 4014.3598 VOLUME = 132608.2186
EPOLZ = -34232.9923
Dipole convergence: rms = 0.849E-02 temperature = 0.64
Density = 1.1683
.............................................................................................................
NSTEP = 800000 TIME(PS) = 1000.000 TEMP(K) = 298.80 PRESS = 251.7
Etot = -56147.4163 EKtot = 9179.7183 EPtot = -65327.1346
BOND = 195.3792 ANGLE = 565.8920 DIHED = 792.3114
1-4 NB = 288.4174 1-4 EEL = 3214.8930 VDWAALS = 39400.5116
EELEC = -94233.5285 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 4176.0672 VIRIAL = 3458.3833 VOLUME = 132069.5300
EPOLZ = -15551.0107
Dipole convergence: rms = 0.170E+00 temperature = 213.88
Density = 1.1731
A V E R A G E S O V E R 800000 S T E P S
NSTEP = 800000 TIME(PS) = 1000.000 TEMP(K) = 299.69 PRESS = 0.9
Etot = -64149.7215 EKtot = 9207.1324 EPtot = -73356.8539
BOND = 209.7879 ANGLE = 560.4803 DIHED = 799.6466
1-4 NB = 285.4319 1-4 EEL = 3207.3750 VDWAALS = 39000.6927
EELEC = -93953.0514 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 4196.7611 VIRIAL = 4194.1818 VOLUME = 132578.1940
EPOLZ = -23467.2168
Dipole convergence: rms = 0.128E+00 temperature = 123.62
Density = 1.1686
Thanks a lot for your help
S. Crouzy
Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux
Département des Interfaces pour l’Energie, la Santé et l’Environnement
Institut de Recherche Interdisciplinaire de Grenoble
CEA Grenoble UMR CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K pièce 110
Tel (33) 438782963
Fax (33) 438785487
http://big.cea.fr/drf/big/english/CBM/GMCT
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Received on Tue Jul 23 2019 - 05:00:02 PDT
