Re: beta column

Date: Fri Sep 10 2010 - 04:25:10 CDT


If you're using FIXED atoms, then their positions won't change at all
along the the simulation so you can use your initial pdb file (with
the beta values) as the fixedAtomsFile when you restart.

For the HARMONIC constraints, my understanding (***NAMD programmers
correct me if I'm wrong***) is that two separate files can be invoked,
the conskfile for the force constants (beta column, your initial pdb
file) and another, the consref, with the reference positions
(presumably your .coor file). But if it is harmonic constraints you're
using, why do you want your reference positions to change along the
simulation, anyway?


Quoting Swarna M Patra <>:

> Hi Namd users
> is it possible to assign a value for beta column for protein or lipid to
> write in the output file. so that I can take the output pdb file for my
> constraint file and continue the simulation without stopping. Now after each
> simulation I take the .coor file convert it to pdb and change the beta for
> desired atoms. if anyone knows any other alternative method to give restrain
> in pdb file let me know.
> thanks
> swarna

Elsa S. Henriques                     e-mail:
Investigadora Auxiliar
Biologia Estrutural e Computacional (@CNC)
e Grupo de Química Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Química - Universidade de Coimbra
3004-535 COIMBRA                         Portugal
Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

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