From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Aug 11 2010 - 07:48:29 CDT
Dear Axel,
The force field is an equation right?
If you have an equation which depends on some parameters (which are
the atom coordinates in MD) there are some specific values of
parameters that set this equation to zero.
I don't know how else you would call that structure that has these
specific atomic coordinates and an 0 energy value.
I would call it reference state since Namd computes the energy values
(positive or negative) with respect to that state.
Imagine my point of view as follows
If the force field would have been an harmonic function the reference
state would be the native conformation and this is set to zero in NMA.
Best,
Mert
On Wed, Aug 11, 2010 at 12:35 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Wed, Aug 11, 2010 at 4:15 AM, Mert Gür <gurmert_at_gmail.com> 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.
>
> mert,
>
> 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
> parameters.
>
> 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.
>
> cheers,
> axel.
>
>> Best,
>> Mert
>>
>> On Tue, Aug 10, 2010 at 4:48 PM, C. Navarro <kdefuego_at_gmail.com> 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 akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
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