VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sun Sep 15 2013 - 17:04:51 CDT

Hi,

Dihedral parameters are only read in at the beginning of a run, so the
order of individual terms relative to one another does not matter in
general, as they all get read in before a force or energy are
calculated. The one exception to this is if there are two conflicting
terms (identical atomtypes and periodicity), which NAMD explicitly warns
you about when dynamics starts.

-Josh Vermaas

On 09/15/2013 01:27 PM, surya narayanan chandrasekaran wrote:
> Hi,
>
> This really simple and probably silly question. when i was looking at
> the psf file dihedral angle section its written the same order of
> dihedral atom types as in parameter file before the dihedral datas are
> written from the log file. but when i write my dihedrals from
> optimization the ordering in par file changes. does this makes any
> difference are error. because I was doing dihedral optimisation by
> part by part of the molecule. so whether change in ordering of file
> type will endup with an error during calculation. just wanted to know
> how namd reads the files?..
>
> --
> Suryanarayanan C
> M.S Chemist
>