Re: [AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing

From: Jason Swails <jason.swails.gmail.com> Date: Wed, 27 Feb 2013 06:58:38 -0500

--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
On Feb 26, 2013, at 6:30 PM, Cheng Wang <njuwangcheng.gmail.com> wrote:
> 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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