Hi Jason,
I have tested the sander in amber9 and it gives the same problem with the
same input inpcrd and prmtop.
>From my opinion, I think the error is from the input inpcrd and prmtop.
Initially, I have prepared inpcrd and prmtop of pure water box from sleap
and the NPT simulation is good with density around 1 in 50 ps with sander
in amber9. However it is slow and it doesn't work with pmemd.amoeba.MPI in
amber 12. The error is :
| New format PARM file being parsed.
| Version = 1.000 Date = 05/22/06 Time = 12:10:21
| ERROR: Amoeba code expects prmtop to specify only one Amber atom type
(ntypes)!
Another problem is I can not prepare the inpcrd and prmtop by sleap if I
want to simulation a water box with a ion inside. It always give errors. So
I switch to use tinker and amoeba_parm to prepare input file. But I got the
problem as I report in the previous email.
It seems that someone can prepare the inpcrd and prmtop by sleap with ions
and there is a tutorial. But I didn't find it. If you know, please send me
a link.
Any comments is welcome.
Have a nice day and thanks.
Best,
Cheng
On Wed, Feb 27, 2013 at 6:58 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Do you get the same problems if you run with the serial version?
>
> I can't see anything blatantly wrong with your simulation input, although
> it would probably be best to explicitly set pres0 in your input file. (It
> defaults to 1, but in the interest of trying things it's worth a shot, I
> suppose).
>
> Probably the first thing I should have asked: do all of your pmemd.amoeba
> tests pass? Unfortunately I don't see any that test constant pressure
> (perhaps there's a bug in the virial calculation, or maybe it's not
> expected to work...). Does the same input work with sander?
>
> HTH,
> Jason
>
> --
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Feb 27 2013 - 11:30:03 PST
