From: Li, Hongzhi (holi_at_coh.org)
Date: Mon Nov 09 2009 - 12:18:59 CST
Hello,
It was my first time to run FEP free energy calculation by following the tutorial. I always got the ERROR message at equilibrium or MD run even with the newest version I downloaded today (either nomal V2.7b1 or cuda-enabled):
(I would appreciate if anyone can help me here)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Charm++ fatal error:
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00420022 s
Info: 1.50328 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is fep_wb.cfg
TCL: Running FEP window 1: Lambda1 0.0 Lambda2 0.0000001 [dLambda 1e-07 ]
TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: lambda2
ERROR: lambda
ERROR: fepEquilSteps
ERROR: fepOutFreq
ERROR: fepOutFile
ERROR: fepCol
ERROR: fepFile
ERROR: fep
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Here is my command line: ~/NAMD_CVS_Linux-x86_64/namd2 +idlepoll fep_wb.cfg
My fep.tcl is copied from tutorial.
Here is my conf file:
###################################################
# ALCHEMICAL TRANSFORMATION
###################################################
# INPUT
parameters par_all22_prot.inp
paraTypeCharmm on
exclude scaled1-4
1-4scaling 1.0
# TOPOLOGY
structure solvate.psf
# COORDINATES
coordinates equilibrate_0.coor
bincoordinates equilibrate.coor
# VELOCITIES
velocities equilibrate_0.vel
binvelocities equilibrate.vel
# CELL
extendedSystem equilibrate.xsc
# OUTPUT FREQUENCIES
outputenergies 100
outputtiming 100
outputpressure 100
restartfreq 100
XSTFreq 100
# OUTPUT AND RESTART
outputname alchemy_0
restartname alchemy
binaryoutput no
binaryrestart yes
# PME
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSizeX 36
PMEGridSizeY 36
PMEGridSizeZ 36
# WRAP WATER FOR OUTPUT
wrapAll on
# CONSTANT-T
langevin on
langevinTemp 300.0
langevinDamping 1.0
# CONSTANT-P
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 100
LangevinPistonDecay 100
LangevinPistonTemp 300
StrainRate 0.0 0.0 0.0
useGroupPressure yes
useflexiblecell no
# SPACE PARTITIONING
splitpatch hydrogen
hgroupcutoff 2.8
stepspercycle 20
margin 1.0
# CUT-OFFS
switching on
switchdist 8.0
cutoff 9.0
pairlistdist 10.0
# RESPA PROPAGATOR
timestep 1.0
fullElectFrequency 4
nonbondedFreq 2
# SHAKE
rigidbonds all
rigidtolerance 0.000001
rigiditerations 400
# COM
commotion no
# FEP
source fep.tcl
fep on
fepFile solvate.fep
fepCol B
fepOutFile alchemy.fepout
fepOutFreq 1
# LOOP OVER LAMBDA-STATES
fepEquilSteps 2000
set nSteps 10000
set dLambda 0.1
set init {0.0 0.0000001 0.000001 0.00001 0.0001 0.001 0.01 0.05 0.1}
set end {0.9 0.95 0.99 0.999 0.9999 0.99999 0.999999 0.9999999 1.0}
runFEPlist $init $nSteps
runFEP 0.1 0.9 $dLambda $nSteps
runFEPlist $end $nSteps
Best regards,
Hogan
---------------------------------------------------------------------
SECURITY/CONFIDENTIALITY WARNING:
This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender.
---------------------------------------------------------------------
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:28 CST