Hello all,
As a test, I ran a short trajectory with sander and then used sander to reprocess the same trajectory to try to get the same energies. The prmtop and inpcrd files were the same. It was disturbing to see that the energies were different.
The closest thing I found to this topic was,
http://archive.ambermd.org/201110/0492.html
In any case, is there a way to ensure that energies in the mdout file are consistent with the energies of the coordinates in the mdcrd file?
I want to do importance sampling and it is crucial to get the correct potential energies!
Thanks!
David Minh
Brief equilibration for energy test
&cntrl
imin=0, ! no minimization
ntx=1, ! read formatted crd file with no velocity information
nscm=1000, ! remove center-of-mass coordinates
ntb=0, ! no periodicity and no PME
dt=0.002, ! 2 fs time step
ntc=2, ! SHAKE
ntf=2, ! omit interactions with H-atoms
cut=1000.0, ! no cutoff (>999.0)
ntt=3, ! Langevin thermostat
ig=50, ! use same random number seed
gamma_ln = 1.0, ! collision frequency in ps^{-1}
temp0=300.0, ! 300 K
igb=5, ! Updated OBC implicit solvent
saltcon=0.025, ! 25 mM salt
nstlim=5000, ! 10 ps of simulation
ntwx=50, ! Write mdcrd every 0.1 ps
ntpr=50, ! Write energy information every 0.1 ps
ioutfm=1, ! Binary NetCDF output
/
Calculate GB energies
&cntrl
imin=5, maxcyc=1, ncyc=0, ! read trajectory in for analysis
ntx=1, ! input is read formatted with no velocities
ntb=0, ! no periodicity and no PME
idecomp=0, ! no decomposition
ntc=2, ! SHAKE
ntf=2, ! omit interactions with H-atoms
cut=1000.0, ! no cutoff (>999.0)
nsnb=99999, ! don't update non-bonded list
temp0=300.0, ! 300 K
igb=5, ! Updated OBC implicit solvent
saltcon=0.025, ! 25 mM salt
ntwe=1, ! Write extensive energy information every step
ioutfm=1, ! Binary NetCDF output
/
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Received on Fri Mar 09 2012 - 14:00:02 PST
