Re: positive total energy

From: Axel Kohlmeyer (
Date: Wed Aug 11 2010 - 04:35:43 CDT

On Wed, Aug 11, 2010 at 4:15 AM, Mert Gür <> wrote:
> The energies are evaluated with respect to an reference state
> (reference energy). Therefore it is possible that you observe both
> positive an negative energies.


what do you mean by "reference state". namdenergy does not
compare the result to anything, it just creates in input file for namd,
writes out the selected atoms to a matching coordinate and psf file,
runs namd and parses the result. as such the interactions are
computed directly according to the force field from the force field

now, if you take away the protein solvent interactions, that may
result in a significant change of the total energy, particularly if
the protein has overall strong interactions with the solvent.
also, for a single snapshot taken arbitrarily from an ongoing
simulation, it is quite possible, that the protein conformation
for away from its ground state and thus of higher potential energy.


> Best,
> Mert
> On Tue, Aug 10, 2010 at 4:48 PM, C. Navarro <> wrote:
>> Hello all,
>> I'm having some trouble trying to understand if it can be OK to have
>> positive energy for a protein during molecular dynamics with namd.  I'm
>> afraid my phisics and termodinamics skills are not enough to answer this
>> question by myself, so I'm putting it to this list.
>> After 1 ns dynamics of a cytosolic protein (in water), I have taken the
>> dcd file and opened in vmd, then calculated the intramolecular energy of
>> the protein for every frame, with this tcl commands:
>> set sel [atomselect top "protein"]
>> package require namdenergy
>> namdenergy -all -sel $sel -ofile protein-energy.dat
>> Giving me positive total energies.  It is important to say that this is
>> happening only with one copy of three? of my protein of study, (The
>> other two proteins show negative energy values); so it is hard to me to
>> think in an error during the dynamics protocol.   By the way, the total
>> energy of the system (taking all the atoms for the energy evaluation),
>> still gives negative values (which is fine).
>> Please, any input to this issue would be very appreciated.
>> Cheers.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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