Jason,
That is exactly what I wanted to know. Although, that does seem like a
rather important subtlety of AMBER.
As a follow up, is there a more direct route to getting this information?
Since I'm not using the TI code (can I even mix that with the HREMD code?)
I can't use the mbar flags, which would probably be my first choice. If
there were someway to just print out the electrostatic energy involving a
certain atom selection, that would work too (in fact that is essentially
what the TI code does, but with the total energy, right?)
As for the 0s, this is just a LJ particle in a water box, so the only bonds
are in water, and ntf=2 suppresses all of that output :) Like I said, this
was a really simple test case to make sure the protocol would work.
Thanks,
Brian
On Fri, Apr 20, 2012 at 11:41 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Why are all of your energy terms 0 except nonbondeds?
>
> Also, the snapshots from the trajectory will be a time step ahead of the
> energies in the mdout file (because energies are calculated, coordinates
> updated, and then printing is done), so I wouldn't expect the energies to
> match up exactly.
>
> If you want to verify actual energies, you should print snapshots every
> frame and then compare the energies from imin=5 on snapshot i to the
> energies in the mdout on step i+1. That should give you a better estimate
> (I'm not sure if I made sense just there...)
>
> All the best,
> Jason
>
> On Fri, Apr 20, 2012 at 10:46 AM, Brian Radak <radak004.umn.edu> wrote:
>
> > Hi everyone,
> >
> > For MBAR analysis I need to calculate the energy of several trajectories
> > using the prmtops from other simulations. I expect there will be some
> > discrepancy in energy because the simulations use double precision and
> the
> > NetCDF files are in single(?) precision, but I don't know how much. As a
> > check on this, I recalculated the energy with same prmtop as the one that
> > generated the trajectory (this should remove the error during comparison
> > anyway right?). However, I think I'm seeing a several kcal/mol
> difference,
> > which seems too high to me, but I could also be comparing the wrong
> > structures/energies. Does anyone see something wrong here?
> >
> > >From dynamics (ntwx = 500):
> >
> > NSTEP = 500 TIME(PS) = 601.000 TEMP(K) = 307.02 PRESS =
> > 0.0
> > Etot = -20117.6204 EKtot = 4832.0403 *EPtot =
> > -24949.6607*
> > BOND = 0.0000 ANGLE = 0.0000 DIHED =
> > 0.0000
> > 1-4 NB = 0.0000 1-4 EEL = 0.0000 *VDWAALS =
> > 3722.3892*
> > *EELEC = -28672.0499* EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > Ewald error estimate: 0.4011E-04
> >
> >
> ------------------------------------------------------------------------------
> >
> > The FIRST energy printout when using imin = 5 with the SAME prmtop and
> the
> > mdcrd file as -y:
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 *-2.4959E+0*4 1.3900E+01 7.1542E+01 O 4601
> >
> > BOND = 0.0000 ANGLE = 0.0000 DIHED =
> > 0.0000
> > *VDWAALS = 3730.5768* *EEL = -28689.6470* HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 0.0000
> >
> > Here is the input for dynamics:
> > production for TI/FEP
> > &cntrl
> > nstlim = 600000, dt = 0.002,
> > ntpr = 500, ntwx = 500,
> > ntwr = 600000,
> > ioutfm = 1, iwrap = 1,
> > ntc = 2, ntf = 2, tol = 1e-8,
> > cut = 10,
> > ntt = 2, temp0 = 310.0, tempi = 310.0, vrand = 2000
> > /
> > &ewald
> > ew_type = 0, order = 6,
> > nfft1 = 50, nfft2 = 50, nfft3 = 50
> > /
> >
> > And the input for re-calculating the energy
> > Calculate Energy with other Hamiltonian for TI/FEP
> > &cntrl
> > imin = 5,
> > maxcyc = 1,
> > ioutfm = 1,
> > ntf = 2,
> > cut = 10
> > /
> > &ewald
> > ew_type = 0, order = 6,
> > nfft1 = 50, nfft2 = 50, nfft3 = 50
> > /
> > ==================
> >
> > Dropbox links to the actual output files:
> >
> > http://dl.dropbox.com/u/40984968/TIP3P_000q_noHREMD_production_1.out
> >
> > http://dl.dropbox.com/u/40984968/TIP3P_000q1_000q2_1.out
> >
> >
> > Thanks,
> > Brian
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri Apr 20 2012 - 09:30:03 PDT
