From: Reza Salari (resal81_at_gmail.com)
Date: Tue May 17 2016 - 14:20:32 CDT
Hi Giacomo,
I repeated my test simulation without colvars and it seems that the problem
still persists. I provided more info here:
https://gist.github.com/resal81/250d65964d72dd85759a26e8b9bb0a20
Reza
=========================================
Reza Salari, M.D. Ph.D.
Postdoctoral Researcher
Center for Computational and Integrative Biology
Rutgers University
Science Building
Camden, NJ 08102
(856) 225-6492
=========================================
On Mon, May 16, 2016 at 7:51 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> 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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