Re: namdEnergy gives significantly different values from those in log file?

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Nov 23 2008 - 12:33:56 CST

By the way, regarding the text below... I do not think that you should
be taking the energies of a subset of your system to use in the
analysis. You really ought to be using the total energy of your system
for doing the type of analysis that you're doing; otherwise you're
basically cherry-picking part of the total energy of your system without
regard for the system as a whole. There are several variants of WHAM for
analyzing replica exchange data in the literature that should be
applicable to your problem. Also, the namd replica exchange scripts
don't contain a pressure correction (Chem. Phys. Lett. 335:435439.), so
you should be running each simulation at constant volume unless you've
added it...
Best,
Peter

Steven Samuel Plotkin wrote:
>
> Dear NAMD users,
>
> I have run namdEnergy on a dcd file, printing out All energies. First
> I noticed the kinetic energy was not printed, then I compared the
> "TOTAL" potential energy from namdEnergy with the TOTAL energy minus
> the KINETIC energy in my log file. The two are quite different --
> about 370 kcal/mol on average. I'm confused by this, I'm not sure what
> is being calculated differently? I've provided links to my dcd, log,
> namdEnergy settings, and conf file are below. I've also posted a long
> version of my question below to help put it in context.
>
> (I'm using namd 2.6 and vmd 1.8.6).
>
> Thanks for any help,
>
> Steve P.
>
>
> FILES:
> log and dcd file:
> http://www.physics.ubc.ca/~steve/NAMD/Repx/fold_dse2.job0.0.log
> http://www.physics.ubc.ca/~steve/NAMD/Repx/fold_dse2.job0.0.dcd
>
> Conf files:
> http://www.physics.ubc.ca/~steve/NAMD/Repx/fold_dse2.conf
> http://www.physics.ubc.ca/~steve/NAMD/Repx/dse2_base.namd
>
> Screenshot of my namdEnergy gui, with settings:
> http://www.physics.ubc.ca/~steve/NAMD/Repx/Screenshot-NAMDEnergy.png
>
> xsc file (if needed):
> http://www.physics.ubc.ca/~steve/NAMD/Repx/fold_dse2.job0.0.xsc
>
>
>
> /Long version of my question:/
>
> I have been able to modify the Alanin replica exchange tcl code to run
> on a small peptide which has been solvated and is in ionic solution. I
> am using namd 2.6 on an x86_64 amd cluster. I ran 16 replicas on 8
> CPUs across 2 nodes of a cluster, with temperatures ranging from 280K
> to 440K. My conf file has some new information not in the alanin
> example because of my solvated box: I have cellBasisVectors,
> wrapWater, wrapAll, PME, and Pressure control options including
> langevinPiston. I was careful to choose the langevinPistonTemp to be
> $NEWTEMP in replica_exchange.tcl.
>
> I want to construct a free energy profile for the small peptide.
> However this must be obtained at one (target) temperature, so I
> reweighted all states by what their Boltzmann weights should have been
> at the target temperature. This doesn't work for me: because the
> system includes the peptide plus the whole water box, after
> re-weighting, one particular state ends up having all the Boltzmann
> weight in the partition function. I didn't think this was feasible.
>
> So then what I must use is the total energy (KE +PE) of the protein
> itself, which includes self interactions /plus/ interactions with
> water and ions. Then I can reweight these energies at the target
> temperature and get a new partition function and free energy profile.
> I thought namdEnergy would be the tool for this.
>
> As a sanity check, I ran namdEnergy on one of my dcd files, printing
> out 'All' energies. First I noticed the kinetic energy was not
> printed, then I compared the "TOTAL" potential energy with the TOTAL
> energy minus the KINETIC energy in my log file. The two are quite
> different -- about 370 kcal/mol on average. However the average total
> potential energy is about 4460 kcal/mol, so the mean error is about
> 8%. Am I doing something wrong here? Or is this to be expected?
>
> At the end of the day what I believe I want is simply the namdEnergy
> numbers for selection 1= PROTEIN , selection 2= "everything else",
> added to the PROTEIN-PROTEIN namdEnergies. However the errors present
> in my sanity check are giving me pause that the namdEnergies are
> trustable.
>
>

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