From: Brian Radak (bradak_at_anl.gov)
Date: Fri May 20 2016 - 07:47:33 CDT
Nothing looks particularly wrong there. The only "strange" thing is the
accumulation of average alchemical force during TI, but it is always
assumed that this will get masked out during integration.
Since you only have one alchemical group, it should be trivial to
compare forces and energies with a non-alchemical run. However these
will, in general, only match exactly with "alchDecouple off" and
"alchBondDecouple on" while you have the opposite settings I believe (we
chose terrible output vocabulary for that). Unless you really know what
you are wanting to calculate, I recommend those settings anyway.
Let me know if that doesn't help,
Brian
On 05/19/2016 05:21 PM, Reza Salari wrote:
> Hi Brian,
>
> Sure. I ran a quick test with the updated parameters (as you
> suggested) and put the ti.out and logfile here:
> https://gist.github.com/resal81/250d65964d72dd85759a26e8b9bb0a20#gistcomment-1782098
> .
>
> Best,
> 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 Wed, May 18, 2016 at 2:25 PM, Brian Radak <bradak_at_anl.gov
> <mailto:bradak_at_anl.gov>> wrote:
>
> 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-${NAMD_VERSION}_Source.tar.gz
>> tar xzf NAMD_CVS-${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 <tel:%28630%29%20252-8643>
> brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
>
>
-- 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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