From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri May 20 2016 - 10:25:03 CDT
Looking at the code again, I just noticed this: Controller::outputFepEnergy
and Controller::writeFepEnergyData don't use the same expression for dE -
one is missing the bonded terms. This explains the discrepancy, it is fixed
by:
Index: src/Controller.C
===================================================================
RCS file: /namd/cvsroot/namd2/src/Controller.C,v
retrieving revision 1.1314
diff -r1.1314 Controller.C
2994c2994,2996
< BigReal dE = eeng_f + ljEnergy_f - eeng - ljEnergy;
---
> BigReal dE = bondedEnergy_f + electEnergy_f + electEnergySlow_f +
ljEnergy_f
> - (bondEnergy + angleEnergy + dihedralEnergy +
improperEnergy
> + electEnergy + electEnergySlow + ljEnergy);
Maybe we need unit tests for these things. If only we had an occasion to
meet and discuss issues with NAMD development...
Jerome
On 20 May 2016 at 14:47, Brian Radak <bradak_at_anl.gov> wrote:
> 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>
> 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> 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>
>> 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>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>
>>>> 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-$>
>>>>> http://www.ks.uiuc.edu/Research/namd/cvs/download/741376/NAMD_CVS-$
>>>>> {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>
>>>>> 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>
>>>>> 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>
>>>>> 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>
>>>>> 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 <%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 <%28630%29%20252-8643>
>> 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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