Re: Excessively high dE_avg values in FEP output (NAMD CVS)

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon May 16 2016 - 18:51:55 CDT

Hi Reza can you post the complete output of NAMD (including colvars output)?

The error could come from the latest NAMD, the latest colvars snapshot (not
merged into NAMD yet), or by an interaction between the two.

Although you probably want to keep the colvars restraints to continue your
production run, it may also be a good idea to disable colvars and see if
this will gives a consistent behavior between NAMD 2.11 and CVS.

Giacomo
On May 16, 2016 5:30 PM, "Reza Salari" <resal81_at_gmail.com> wrote:

> 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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