sleap was deprecated (that's why it's not part of AmberTools 12).
As for the amoeba problems, I really cannot be of help given my (almost)
complete lack of experience with it.
Good luck,
Jason
On Wed, Feb 27, 2013 at 2:16 PM, Cheng Wang <njuwangcheng.gmail.com> wrote:
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 27 2013 - 11:30:05 PST
