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From: Brian Radak <radak004.umn.edu>

Date: Fri, 20 Apr 2012 12:03:41 -0400

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
*

*>
*

Date: Fri, 20 Apr 2012 12:03:41 -0400

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:

-- ================================ 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/amberReceived on Fri Apr 20 2012 - 09:30:03 PDT

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