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

From: Brian Radak (bradak_at_anl.gov)
Date: Wed May 18 2016 - 13:25:44 CDT

Thanks for the notice Jerome.

Yes, that is quite possibly a bug. I admittedly have not been as careful
with the FEP code base while implementing the new bonded scaling code, etc.

Reza -
Can you try the same calculation using "alchType TI" and using the same
seed value? You can send me the output logs for 10 steps or so off list
(also set outputEnergies 1 and alchOutFreq 1, if you would). I will be
worried (and act with haste accordingly) if the energies diverge very
quickly. Divergence of the alchemical force should also indicate if some
other problem is at play.

Cheers,
Brian

On 05/17/2016 02:44 PM, Jérôme Hénin wrote:
> Yup, this isn't a colvars issue, I think it may have to do with the
> recent alchemy improvements by Brian Radak. Let me CC him to get his
> attention... :-)
>
> Jerome
>
> On 17 May 2016 at 21:20, Reza Salari <resal81_at_gmail.com
> <mailto:resal81_at_gmail.com>> wrote:
>
> 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 <mailto: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
> <mailto: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-${NAMD_VERSION}_Source.tar.gz
> <http://www.ks.uiuc.edu/Research/namd/cvs/download/741376/NAMD_CVS-$%7BNAMD_VERSION%7D_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 <tel:%28856%29%20225-6492>
> =========================================
>
>
>

-- 
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov

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