New NAMD version 2011-03-03 uses

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Tue Mar 15 2011 - 09:52:27 CDT

Hi all,
I have the new NAMD version from 2011-03-03 and was wondering
if someone could briefly outline if there are any major changes
to the necessary input file used (e.g. variable name changes)?

I am specifically interested in the free energy perturbation formalism.
I have done some runs with the new version using the following input

# FEP
source ./fep.tcl
alch on
alchType fep
alchFile system.fep
alchCol B
alchOutFile out.fepout_1
alchOutFreq 500

alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdwShiftCoeff 5.0
alchDecouple yes

alchEquilSteps 37500 ; # 75ps
set nSteps 75000 ; # 150ps

runFEP 0.0 1.0 0.0625 $nSteps ; # 10 windows outward

Also, I am interested in whether there have been developments
in how namd can deal with the error analysis of the simulation.
Is there a way of outputting ÄU values during the simulation (to
obtain an idea of the probability distribtions P(ÄU) of the simulation)?
Ultimately I wish to obtain an estimate of the simulation bias.

Thank you for any input here
Christian

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