From: Reza Salari (resal81_at_gmail.com)
Date: Mon May 16 2016 - 12:42:27 CDT
Hi,
I'm running some tests using NAMD cvs and the latest colvars on Stampede
(compile script attached below) and noticed very large dE_avg (and
subsequently dG) values in the fepout files:
STEP Elec vdW
dE dE_avg Temp dG
# l l+dl l
l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 0.89 LAMBDA2 0.9
FepEnergy: 50 -172948.7128 -172948.7462 3821.4453
3822.1917 0.7129 -36458.2406 300.2047 -9999999999.9999
FepEnergy: 100 -172545.4504 -172545.4839 3375.0287
3375.7949 0.7328 -36445.1885 301.0309 -9999999999.9999
FepEnergy: 150 -173167.4969 -173167.5303 3786.2865
3786.9088 0.5888 -36445.1217 302.0768 -9999999999.9999
FepEnergy: 200 -172776.3445 -172776.3780 3466.1294
3466.9678 0.8050 -36458.5775 301.4277 -9999999999.9999
FepEnergy: 250 -172866.1536 -172866.1870 3604.4608
3605.2236 0.7293 -36456.9526 300.7179 -9999999999.9999
I think this is a bug - possibly because dE_avg initially is not set to dE
value of the first step. In the meantime the dG values are recoverable by
using dE and Temp directly.
Best Regards,
Reza Salari
#===================================================
*System*: Stampede
*Loaded modules:*
$ module list
1) intel/15.0.2 2) mvapich2/2.1 3) xalt/0.6 4) TACC
#===================================================
#!/usr/bin/env bash
set -e
NAMD_VERSION="2016-05-09"
download_namd () {
wget
http://www.ks.uiuc.edu/Research/namd/cvs/download/741376/NAMD_CVS-${NAMD_VERSION}_Source.tar.gz
tar xzf NAMD_CVS-${NAMD_VERSION}_Source.tar.gz
ln -s NAMD_CVS-${NAMD_VERSION}_Source namd_cvs
}
download_colvars () {
wget https://github.com/colvars/colvars/archive/master.zip
unzip master.zip
ln -s colvars-master colvars
}
download_fftw_tcl () {
cd namd_cvs
wget
http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz
tar xzf fftw-linux-x86_64.tar.gz
ln -s linux-x86_64 fftw
wget
http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz
tar xzf tcl8.5.9-linux-x86_64.tar.gz
ln -s tcl8.5.9-linux-x86_64 tcl
wget
http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64-threaded.tar.gz
tar xzf tcl8.5.9-linux-x86_64-threaded.tar.gz
ln -s tcl8.5.9-linux-x86_64-threaded tcl-threaded
cd ..
}
patch_namd () {
cd colvars
./update-colvars-code.sh -f ../namd_cvs
cd ..
}
compile_charm () {
cd namd_cvs
tar xf charm-*
cd charm-*
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared
--with-production
cd ../..
}
config_namd () {
cd namd_cvs
./config Linux-x86_64-icc --charm-arch mpi-linux-x86_64
cd ..
}
compile_namd () {
cd namd_cvs
cd Linux-x86_64-icc
make depends
make -j 4 release
cd ../..
}
download_namd
download_colvars
download_fftw_tcl
patch_namd
compile_charm
config_namd
compile_namd
#===================================================
=========================================
Reza Salari, M.D. Ph.D.
Postdoctoral Researcher
Center for Computational and Integrative Biology
Rutgers University
Science Building
Camden, NJ 08102
(856) 225-6492
=========================================
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