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

From: Steven Samuel Plotkin (
Date: Mon Nov 24 2008 - 01:01:21 CST

Dear Peter,
Thanks for your observations. Regarding the energetic components of
NAMDEnergy and the logfile, everything is essentially the same except
for ELECTrostatic interactions.
So this is likely due then to the difference in the default values of
1-4scaling in NAMDEnergy and in my conf file? 1-4 atoms in my simulation
have .4 of their electrostatic energy apparently. My 1-4scaling is .4
because I unfortunately did not change the 1-4scaling value from that in
the alanin example for replica exchange...

It seems more sensible to re-run the simulation with 1-4scaling set to 1
than to adjust the NAMDEnergy generated conf file, but after thinking
more about your comments in your other reply, I do not think using
NAMDEnergy for part of the system is what I want to do at all. I'll post
a separate reply there.

(BTW- on a completely different note, I am getting duplicate emails of
all NAMD forum posts because I believe I am subscribed both as steve(at)
physics(dot)ubc(dot)ca and steve (at) phas (dot) ubc (dot) ca. Our
department domain name changed but all email is still forwarded. Is
there a way to unsubscribe me from say the physics domain? The is my newer email. Sorry I don't know how else to go about
this, if I unsubscribe from my present email I unsubscribe the newer
domain and keep the outdated domain. )


Peter Freddolino wrote:
> 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.
>> log and dcd file:
>> Conf files:
>> Screenshot of my namdEnergy gui, with settings:
>> xsc file (if needed):
>> /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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