Cylindrical harmonic BC and constraintScaling

From: Elsa Fernanda de Sousa Henriques (
Date: Mon Apr 20 2009 - 05:22:25 CDT


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


"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 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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