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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Received on Fri Apr 20 2012 - 08:00:03 PDT
