From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Thu Apr 29 2010 - 07:39:49 CDT
Thanks for your kind analysis.
The dielectric constant of a protein is about 2 to 4, thus when the protein is polarizable, a proper dielectric constant bigger than 1.0 should be adopted to reduce the intensity bwteen two charged atoms. Should we?
If this is the case, i can abtain the same values as what namd got.
Appreciate your attention!
å¨2010-04-29 15:59:42ï¼"JÃ©rÃ´me HÃ©nin" <jhenin_at_ifr88.cnrs-mrs.fr> åéï¼
>> 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?
>Maybe. In the CHARMM ff, the rule is to include nonbonded terms for
>all atoms except those linked through one or two bonds (which will
>typically be coupled by bond and angle terms). Atoms connected by a
>torsion term (3 bonds) have their full nonbonded interactions (the
>so-called 1,4-interactions). There are a few exceptions: for some atom
>types, the CHARMM parameter files list modified Lennard-Jones
>parameters for 1,4 interactions. Electrostatics is never modified,
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