From: GALLY Jose Manuel (jose.manuel.gally_at_gmail.com)
Date: Thu Jun 27 2013 - 02:12:24 CDT
Dear all,
I am currently trying to run some bidirectional FEP calculations using NAMD
to do a single mutation (Asp to Asp for testing) in a protein. The
calculations were achieved without any error.
But there are few things I don't understand...
First of all, I get a variation of free energy of about 100kcal/mol during
the process, which is a really high value since I would expect a null
value.
The system is equilibrated at NVT to 300K during 50 ps then NPT to 1atm
during 50 ps.
Secondly, I tried to improve the convergence at λ=0 by increasing the
number of steps (numSteps=25000-30000-35000) and the number of windows
(dλ=0.025-0.020),
but I unexpectedly obtained worse results since the hysteresis keeps on
growing during the whole backward calculation. Please find attached the
corresponding summary files.
I don't see what I am doing wrong... Any help would be much appreciated!
Thanks in advance,
José-Manuel
Technical notes:
NAMD version: 2.9_Linux-x86_64 multicore
Solvation: Explicit solvent
Tool to generate summary files: parseFEP 1.8 from VMD 1.9.1
Part of the config file:
forward
#############################################################
## FEP PARAMETERS ##
#############################################################
source ../commonFilesForFEP/fep.tcl
alch on
alchType FEP
alchFile 0-Input/ionized.fep
alchCol B
alchOutFile 6-Output/AsptoAsp_4-FEPforward.fepout
alchOutFreq 10
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdwShiftCoeff 5.0
alchDecouple yes
set init { 0.00001 0.0001 0.001 0.01 0.025 0.05 0.075 0.1 }
set end { 0.9 0.925 0.95 0.975 0.99 0.999 0.9999 0.99999 }
set dLambda 0.025
alchEquilSteps 4000
set numSteps 25000
runFEPlist $init $numSteps
runFEP 0.1 0.9 $dLambda $numSteps
runFEPlist $end $numSteps
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