From: 岡部篤俊 (atsutoshi0708_at_gmail.com)
Date: Tue Aug 18 2015 - 09:54:40 CDT
I have question about lambda-exchange multiple-copy alchemical free energy calculation.
This is my first try to use this method on NAMD 2.10, so I want to do test calculation using sample scripts in /NAMD_2.10_Source/lib/replica/FEP_wca directory.
Following readme.txt, I prepared my ouput directories.
./make_output_dirs.sh output_solv 36
After that, run simulation.
mpirun -np 36/NAMD/NAMD_2.10_Source/Linux-x86_64-g++/namd2 +replicas 36 fep_solv.conf --source FEP_wca.namd +stdout output_solv/%d/job0.%d.log
Then, I got the error message in output_solv/0/job0.0.log below.
Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (16-way SMP).
Charm++> cpu topology info is gathered in 0.013 seconds.
Info: NAMD 2.10 for Linux-x86_64-MPI
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Based on Charm++/Converse 60601 for mpi-linux-x86_64
Info: Built Fri Feb 6 20:08:55 CST 2015 by okabe on clb126
Info: 1 NAMD 2.10 Linux-x86_64-MPI 1 leon301 okabe
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.03073 s
Info: 412.543 MB of memory in use based on /proc/self/stat
Info: Configuration file is fep_solv.conf
Info: Working in the current directory NAMD/NAMD_2.10_Source/lib/replica/FEP_wca
Info: Command-line argument is --source FEP_wca.namd
TCL: Reduction callback proc set to save_callback
TCL: Suspending until startup complete.
ERROR: 'alchLambda' is a required configuration option
ERROR: when 'alch' is set
ERROR: alchLambda defines: Coupling parameter value
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
 Stack Traceback:
Could you advice me how to run this method?
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