From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Feb 10 2011 - 13:01:33 CST
Your problem is not actually dihedrals, it's the CMAP cross-terms.
*Those* are asymmetric, of course. The problem is, by default NAMD
just sums those into the dihedral energy. The "mergeCrossterms" option
must be deactivated to get them separately.
To prepare CMAP data for D-aminoacids, look there:
On 9 February 2011 21:40, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> wrote:
> Hi Keith,
> CHARMM dihedral energy terms are symmetric iff the phase parameter
> delta is 0 or 180 degrees. Which it is, at least in the standard
> peptide force field.
> I've just run a test with a small peptide, and got exactly the same
> result. How did you prepare the input coordinates?
> On 9 February 2011 20:23, Keith Battle <keith.battle_at_gmail.com> wrote:
>> Hi NAMD world,
>> I performed a minimization using the CHARMM force field of a single
>> L-Aspartate in vacuum using NAMD 2.7. I also performed the same
>> minimization of a single D-Aspartate. On the 0th step, the total
>> energy and the dihedral energy are different by about 7 kcal/mol. All
>> other energies are the same (bond, elec, etc.). Are there any ideas as
>> to why this may be the case? I performed the same procedure in QUANTA
>> with the CHARMM force field and the total energy for L and D are the
>> Keith Battle
>> Research Technician
>> University of South Alabama
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