Re: Cylindrical harmonic BC and constraintScaling

From: Elsa Fernanda de Sousa Henriques (
Date: Mon Apr 20 2009 - 08:25:20 CDT

Hi again,

Please ignore my previous mail; already figured out what went wrong.
Sorry for the inconvenience,


On Mon, April 20, 2009 12:22 pm, Elsa Fernanda de Sousa Henriques wrote:
> Hi,
> I'm trying to simulate a system using both cylindrical harmonic BC to
> confine the solvent and some harmonic restraints on my protein's backbone
> which I try to loosen up along the simulation using constraintScaling till
> the backbone constraints come to zero.
> My question is, does the constraintScaling parameter affect also the
> cylindricalBCk# ? (looks like, for when my constraintScaling = 0.0 the
> BOUNDARY energy drops to zero ... and I end up with a couple of waters
> 'vaporizing'). If so, is there a way around it (besides modifying the
> consKFile as the simulation progresses)?
> Any feedback will be greatly appreciated, tnx
> Elsa

 "While Time,
  The endless idiot, runs screaming round the world."

                       –in Carson McCullers' Voices
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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