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

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Nov 23 2008 - 01:55:51 CST

Hi Steve,
if you compare the components generated by namdenergy and your original
run, do you find any columns that are consistently the same or different?
BTW, why is your 1-4scaling 0.4? NAMDEnergy uses a default value for
this setting (1.0 for charmm input files, 0.83333 for amber). You may
need to modify the namdenergy-produced config files for your purposes...
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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