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.
> _______________________________________________
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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 Fri Apr 20 2012 - 09:00:04 PDT
