From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Wed Apr 28 2010 - 22:54:30 CDT
Well, here comes another question more detailed, that:
Based on the CHARMM22 force field, i use my own code to roughly minimize a peptide and compare each term of interactions with the results of minimization of namd2.6. My approachment is simply to set velocity zero everay step, which is inferior to annealing algorithm that namd may adpot.
All interactions are comparable and consistent with the results of namd except for electrostatic interaction when dielectric constant is 1.0, the absolute value of which by my code is nearly twice as big as that by namd.
As to VDW and Electrostatic interactions, all pairs of atoms without bond interaction( bond stress, angle bend, dihedral torsion, improper dihedral) are considered in my code. I did not use cut-off method. Can you find something wrong?
Thanks for your time!
在2010-04-29 00:17:58，"Axel Kohlmeyer" <akohlmey_at_gmail.com> 写道：
>2010/4/27 ydhuang2727 <ydhuang2727_at_163.com>:
>> Dear NAMD developers,
>> Will you please tell me what the dielectric constant NAMD uses in the
>> Comlombic potential, when i simulate a protein in vacuum. Is it still 1.0?
>yes. why should it be any different?
>an MD code like NAMD doesn't really know what kind of system
>you feed it. all it sees is positions and interactions between them.
>> Best wishes!
>Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>Institute for Computational Molecular Science
>Temple University, Philadelphia PA, USA.
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