From: Reza Salari (resal81_at_gmail.com)
Date: Mon May 16 2016 - 16:29:32 CDT
Hi,
I'm running some FEP tests on Stampede using the development versions of
NAMD and Colvars (from CVS and github, respectively) 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
The compile script is attached at the end. I think this is a bug - possibly
because dE_avg is not initially set to the 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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