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Development version of plumed 2
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error in reweight procedure #1019

Open gekbuccella opened 4 months ago

gekbuccella commented 4 months ago

Dear users, I'm trying to do a reweight of my metaD to assess convergence of FES profile. I followed the procedure described in [https://www.plumed.org/doc-v2.9/user-doc/html/advanced-methods.html#advanced-methods-ex-3]

When I run the command: plumed driver --ixyz geo_end.xyz --plumed plumed_reweight.dat --kt 1.8

I get the following error message:

PLUMED: PLUMED is starting PLUMED: Version: 2.9.0 (git: Unknown) compiled on May 25 2023 at 11:36:13 PLUMED: Please cite these papers when using PLUMED [1][2] PLUMED: For further information see the PLUMED web page at http://www.plumed.org PLUMED: Root: /home/TTD/.conda/envs/dftbplus23.1-nompi/lib/plumed PLUMED: For installed feature, see /home/TTD/.conda/envs/dftbplus23.1-nompi/lib/plumed/src/config/config.txt PLUMED: Molecular dynamics engine: driver PLUMED: Precision of reals: 8 PLUMED: Running over 1 node PLUMED: Number of threads: 1 PLUMED: Cache line size: 512 PLUMED: Number of atoms: 344 PLUMED: File suffix: PLUMED: FILE: plumed_reweight.dat PLUMED: Action RESTART PLUMED: with label @0 PLUMED: MD code didn't require restart PLUMED: Switching on restart PLUMED: Restarting simulation: files will be appended PLUMED: Action UNITS PLUMED: with label @1 PLUMED: length: A = 0.1 nm PLUMED: energy: kj/mol PLUMED: time: ps PLUMED: charge: e PLUMED: mass: amu PLUMED: using physical units PLUMED: inside PLUMED, Boltzmann constant is 0.00831446 PLUMED: Action FLUSH PLUMED: with label @2 PLUMED: with stride 10 PLUMED: Action DISTANCE PLUMED: with label d_C_319-C_318 PLUMED: between atoms 319 318 PLUMED: using periodic boundary conditions PLUMED: Action DISTANCE PLUMED: with label d_C_319-C_328 PLUMED: between atoms 319 328 PLUMED: using periodic boundary conditions PLUMED: Action DISTANCE PLUMED: with label d_C_319-C_325 PLUMED: between atoms 319 325 PLUMED: using periodic boundary conditions PLUMED: Action METAD PLUMED: with label metad PLUMED: with arguments d_C_319-C_328 PLUMED: added component to this action: metad.bias PLUMED: Gaussian width 0.200000 Gaussian height 0.000000 PLUMED: Gaussian deposition pace 10000 PLUMED: Gaussian file HILLS PLUMED: Well-Tempered Bias Factor 40.000000 PLUMED: Hills relaxation time (tau) inf PLUMED: KbT 2.910062 PLUMED: Grid min 0.0 PLUMED: Grid max 10.0 PLUMED: Grid bin 1000 PLUMED: Grid uses spline interpolation PLUMED: added component to this action: metad.rbias PLUMED: added component to this action: metad.rct PLUMED: The c(t) reweighting factor will be calculated every 1 hills PLUMED: Restarting from HILLS: 200 Gaussians read PLUMED: Bibliography [3][4][5] PLUMED: Action PRINT PLUMED: with label @7 PLUMED: with stride 1 PLUMED: with arguments d_C_319-C_318 d_C_319-C_328 d_C_319-C_325 PLUMED: on file colvar-rew.data PLUMED: with format %f PLUMED: END FILE: plumed_reweight.dat PLUMED: Timestep: 1.000000 PLUMED: KbT: 1.700000 PLUMED: Relevant bibliography: PLUMED: [1] The PLUMED consortium, Nat. Methods 16, 670 (2019) PLUMED: [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014) PLUMED: [3] Laio and Parrinello, PNAS 99, 12562 (2002) PLUMED: [4] Barducci, Bussi, and Parrinello, Phys. Rev. Lett. 100, 020603 (2008) PLUMED: [5] Pratyush and Parrinello, J. Phys. Chem. B, 119, 736 (2015) PLUMED: Please read and cite where appropriate! PLUMED: Finished setup PLUMED: PLUMED: ################################################################################ PLUMED: PLUMED: (tools/Grid.cpp:168) PLMD::GridBase::index_t PLMD::GridBase::getIndex(const std::vector&) const PLUMED: Looking for a value outside the grid along the 0 dimension (arg name: d_C_319-C_328) PLUMED: PLUMED: The above exception was the direct cause of the following exception: PLUMED: PLUMED: (core/PlumedMain.cpp:971) void PLMD::PlumedMain::justCalculate() PLUMED: An error happened while calculating metad PLUMED: ################################################################################ PLUMED: Cycles Total Average Minimum Maximum PLUMED: 1 0.263972 0.263972 0.263972 0.263972 PLUMED: 1 Prepare dependencies 1 0.000004 0.000004 0.000004 0.000004 PLUMED: 2 Sharing data 1 0.000055 0.000055 0.000055 0.000055 PLUMED: 3 Waiting for data 1 0.000003 0.000003 0.000003 0.000003 PLUMED: 4 Calculating (forward loop) 1 0.181019 0.181019 0.181019 0.181019 terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError' what(): (tools/Grid.cpp:168) PLMD::GridBase::index_t PLMD::GridBase::getIndex(const std::vector&) const Looking for a value outside the grid along the 0 dimension (arg name: d_C_319-C_328)

The above exception was the direct cause of the following exception:

(core/PlumedMain.cpp:971) void PLMD::PlumedMain::justCalculate() An error happened while calculating metad Aborted

It seems like this is complaining that the biased distance exceeds the grid limits, but actually this is untrue (see colvar.data). I really don't understand what could be the problem. I tought that this could be caused by the fact that I didn't include metad.* in PRINT action in plumed .dat, but I tried with a past simulation in which I did and found the same issue. Please find attached the list of files needed to replicate, except for the trajectory file (geo_end.xyz), which is too heavy to be posted here. I can however share it through other channels if needed.

Thank you in advance for any kind of help Best Giacomo files.zip