Cylindrical harmonic BC and constraintScaling

From: Elsa Fernanda de Sousa Henriques (ehenriques_at_qui.uc.pt)
Date: Mon Apr 20 2009 - 05:22:25 CDT

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

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

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Elsa S. Henriques e-mail: ehenriques_at_qui.uc.pt
Investigadora Auxiliar

Biologia Estrutural e Computacional (@CNC)
e Grupo de Qumica Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Qumica - Universidade de Coimbra
3004-535 COIMBRA Portugal

Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

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