Excessively high dE_avg values in FEP output (NAMD CVS)

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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