Dear Amber Users:
Greetings. I have a problem when I run a pure water box with
pmemd.amoeba.MPI in Amber12.
It is a system with 216 waters (Using watersmall.xyz in Tinker website as
the starting structure)
The input files (prmtop and inpcrd) were prepared with tinker4.3 following
the procedure in
$AMBERHOME/src/pmemd.amoeba/build_amoeba/examples/Organic_liquids/README
I have run the minimization, NPT at 10 K ( this is OK for density) , NVT
to heat the system to 300K then NPT for production (Problem happened here)
The following is for NPT at 300 K
mdin file is the same as in test $AMBERHOME/test/amoeba_wat2/nptverlet
&cntrl
ntx=5, irest=0,
nstlim=10000,
ntpr=100, ntwr=1000,ntave=1000,
nscm=1000,ntwx=0,
dt=0.001, vlimit=10.0,
cut=8.,maxcyc=50,ntmin=2,imin=0,
ntt=3, temp0=300.0,tempi=300.0,taup=2.0,gamma_ln=5.0,
ntp=1,ntb=2, iamoeba=1,
/
&ewald
nfft1=24,nfft2=24,nfft3=24,
skinnb=0.8,nbtell=0,order=5,ew_coeff=0.45,
/
&amoeba
do_amoeba_nonbond=1,do_amoeba_valence=1,beeman_integrator=0,
do_bond=1,do_ureyb=1,do_reg_angle=1,do_trig_angle=1,
do_opbend=1,do_torsion=1,do_str_torsion=1,do_pi_torsion=1,do_strbend=1,
do_torsion_torsion=1,do_induced=1,do_recip=1,do_direct=1,do_adjust=1,
do_vdw=1,do_vdw_taper=1,do_vdw_longrange=1,
do_self=1,dipole_scf_tol = 0.01,dipole_scf_iter_max=30,
sor_coefficient=0.7,ee_damped_cut=4.5,ee_dsum_cut=6.7,
/
Part of mdout:
NSTEP = 0 TIME(PS) = 39.900 TEMP(K) = 309.62 PRESS =
0.0
Etot = -52.3080 EKtot = 598.0450 EPtot =
-650.3530
BOND = 90.2577 ANGLE = 64.9090 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
130.6443
EELEC = -1190.2214 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = -412.8043 VOLUME =
6180.6928
EPOLZ = 254.0575
Dipole convergence: rms = 0.805E-02 iters = 3.00
Density =
1.0455
------------------------------------------------------------------------------
NSTEP = 100 TIME(PS) = 40.000 TEMP(K) = 311.96 PRESS =
3625.5
Etot = -60.0346 EKtot = 602.5590 EPtot =
-662.5936
BOND = 101.8250 ANGLE = 54.6825 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
115.9511
EELEC = -1191.2794 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 602.5590 VIRIAL = 210.8243 VOLUME =
6268.3327
EPOLZ = 256.2272
Dipole convergence: rms = 0.805E-02 iters = 3.00
Density =
1.0308
------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 40.100 TEMP(K) = 294.47 PRESS =
3818.6
Etot = -35.3151 EKtot = 568.7788 EPtot =
-604.0939
BOND = 127.8512 ANGLE = 71.1567 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
84.2403
EELEC = -1140.8546 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 568.7788 VIRIAL = 77.6825 VOLUME =
6343.9643
EPOLZ = 253.5125
Dipole convergence: rms = 0.795E-02 iters = 3.00
Density =
1.0186
------------------------------------------------------------------------------
.....
.....
NSTEP = 9900 TIME(PS) = 49.800 TEMP(K) = 303.61 PRESS =
-79.4
Etot = 89.5063 EKtot = 586.4408 EPtot =
-496.9345
BOND = 155.4463 ANGLE = 79.8979 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
38.8393
EELEC = -1012.5701 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 586.4408 VIRIAL = 1202.0265 VOLUME =
8392.7040
EPOLZ = 241.4520
Dipole convergence: rms = 0.660E-02 iters = 3.00
Density =
0.7699
------------------------------------------------------------------------------
NSTEP = 10000 TIME(PS) = 49.900 TEMP(K) = 297.80 PRESS =
1287.4
Etot = 85.4612 EKtot = 575.2203 EPtot =
-489.7591
BOND = 150.1086 ANGLE = 77.1086 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
38.0968
EELEC = -992.6127 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 575.2203 VIRIAL = 677.6819 VOLUME =
8393.5312
EPOLZ = 237.5395
Dipole convergence: rms = 0.652E-02 iters = 3.00
Density =
0.7698
------------------------------------------------------------------------------
The density is keeping decreasing. In addition, if I keeping running to 1
ns. The density will around 0.02 or something..
I am not sure what is problem.Any comment is welcome.
Best,
Cheng
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Received on Tue Feb 26 2013 - 16:00:02 PST
