GBIS question and possible Bug for colvar "outputSystemForce" declaration in NAMD CVS-2011-03-03

From: Bjoern Olausson (
Date: Tue Mar 22 2011 - 17:56:09 CDT


I a running NAMD CVS-2011-03-03 for Linux-x86_64-ibverbs-net-linux-x86_64-
ibverbs-icc with GBIS, ABF and COLVARS.
So far it seems to work great, except on weird thing:
When I want to turn on "outputSystemForce" I get the following error.

------ Log -------
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputEnergy = on [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: Error: boolean values only are allowed for "outputSystemForce".

Here is an excerp of my config:
------ Config Part -------
  outputSystemForce yes ;# write total system force to the trajectory file
  outputAppliedForce yes ;# write total force applied to the trajectory

For all other parameters you can add a comment behind it via ";# COMMENT"
This does not work for outputSystemForce and outputAppliedForce. As soon you
add a comment as above it will bail out.

Three more question:
Is the temperature control setup for GBIS supposed to be the same as when
running an explicit solvent simulation?

# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp 300
langevinHydrogen off

What about the pressure control? I guess the GBIS implementation will mimic 1
atm pressure.
But when I enable pressure control, my system is rapidly compressed and the
simulation dies with a "FATAL ERROR: Periodic cell has become too small for
original patch grid! [...]" message.
Turning of "Langevin pressure control" solved that problem. Is one supposed to
use "Berendsen pressure control" instead of Langevin - if at all?

# Constant Pressure Control (variable volume)
useGroupPressure yes
useFlexibleCell yes
useConstantArea no
useConstantRatio yes
LangevinPiston off
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp 300

Last question:
Is GBIS compatible with "Advanced Molecular Dynamics"?


Bjoern Olausson
Martin-Luther-Universit├Ąt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:42 CST