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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