[gmx-users] gmx mdrun std::bad_alloc whilst using PLUMED
Nash, Anthony
a.nash at ucl.ac.uk
Tue Nov 17 23:04:31 CET 2015
Hi all,
I am using PLUMED 2.2 and gromacs 5.0.4. For a while I had been testing
the viability of three collective variables for plumed, two dihedral
angles and one centre of mass distance. After observing my dimer rotate
about each other I decided it needed an intrahelical distance between two
of the dihedral atoms (A,B,C,D), per helix, to sample the CV space whilst
maintaining the Œregular¹ alpha-helical structure (the dihedral sampling
was coming from the protein uncoiling rather than rotating). Note: it is
likely that I will change these distances to the built-in alpha helical
CV.
The moment I increased the number of CVs from three to five, gromacs
throws out a memory error. When I remove the 5th CV it still crashes. When
I remove the 4th it stops crashing.
‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
CLUSTER OUTPUT FILE
‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
starting mdrun 'NEU_MUT in POPC in water'
50000000 steps, 100000.0 ps.
-------------------------------------------------------
Program: gmx mdrun, VERSION 5.0.4
Memory allocation failed:
std::bad_alloc
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Halting parallel program mdrun_mpi_d on CPU 0 out of 12
It halts all 12 processes and the job dies. I increased the memory so I am
using 43.2 GB of RAM distributed over 12 processes. The job still fails
(but then, allocation of memory is very different to not having any memory
at all).
The contents of the gromacs.log file only reports the initialisation of
gromacs followed by the initialisation of plumed. After this I would have
expected the regular MD stepping output. I¹ve included the plumed
initialisation below. I would appreciate any help. I suspect the problem
lies with the 4th and 5th CV although systematically removing them and
playing around with the parameters hasn¹t yielded anything yet. Please
ignore what parameter values I have set. Besides the atom number
everything else is a result of me trying to work out where certain ranges
of values is causing PLUMED to exit and gromacs to crash. PLUMED input
file below:
‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
PLUMED INPUTFILE
‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
phi: TORSION ATOMS=214,230,938,922
psi: TORSION ATOMS=785,801,367,351
c1: COM ATOMS=1-571
c2: COM ATOMS=572-1142
COMdist: DISTANCE ATOMS=c1,c2
d1: DISTANCE ATOMS=214,367
d2: DISTANCE ATOMS=938,785
UPPER_WALLS ARG=COMdist AT=2.5 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
LABEL=COMuwall
LOWER_WALLS ARG=COMdist AT=1.38 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
LABEL=COMlwall
UPPER_WALLS ARG=d1 AT=1.260 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
LABEL=d1uwall
LOWER_WALLS ARG=d1 AT=1.228 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
LABEL=d1lwall
UPPER_WALLS ARG=d2 AT=1.228 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
LABEL=d2uwall
LOWER_WALLS ARG=d2 AT=1.196 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
LABEL=d2lwall
METAD ...
LABEL=metad
ARG=phi,psi,COMdist,d1,d2
PACE=1
HEIGHT=0.2
SIGMA=0.06,0.06,0.06,0.06,0.06
FILE=HILLS_neu_mut_meta_A
BIASFACTOR=10.0
TEMP=310.0
GRID_MIN=-pi,-pi,0,0,0
GRID_MAX=pi,pi,2.5,2.5,2.5
GRID_SPACING=0.01,0.01,0.01,0.01,0.01
... METAD
PRINT STRIDE=100
ARG=phi,psi,COMdist,COMlwall.bias,COMuwall.bias,d1,d1lwall.bias,d1uwall.bia
s,d2,d2lwall.bias,d2uwall.bias,metad.bias FILE=COLVAR_neu_mut_meta_A
‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
GROMACS LOGFILE
‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 53575 Atoms
Charge group distribution at step 0: 4444 4474 4439 4268 4913 4471 4298
4519 4395 4584 4474 4296
Initial temperature: 311.436 K
PLUMED: PLUMED is starting
PLUMED: Version: 2.2.0 (git: Unknown) compiled on Nov 6 2015 at 11:15:41
PLUMED: Please cite this paper when using PLUMED [1]
PLUMED: For further information see the PLUMED web page at
http://www.plumed-code.org
PLUMED: Molecular dynamics engine: gromacs
PLUMED: Precision of reals: 8
PLUMED: Running over 12 nodes
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 53575
PLUMED: File suffix:
PLUMED: FILE: neu_mut_meta_A.dat
PLUMED: Action TORSION
PLUMED: with label phi
PLUMED: between atoms 214 230 938 922
PLUMED: using periodic boundary conditions
PLUMED: Action TORSION
PLUMED: with label psi
PLUMED: between atoms 785 801 367 351
PLUMED: using periodic boundary conditions
PLUMED: Action COM
PLUMED: with label c1
PLUMED: serial associated to this virtual atom is 53576
<ATOMS FROM A RANGE - I have removed for clarity>
PLUMED: PBC will be ignored
PLUMED: Action COM
PLUMED: with label c2
PLUMED: serial associated to this virtual atom is 53577
<ATOMS FROM A RANGE - I have removed for clarity>
PLUMED: PBC will be ignored
PLUMED: Action DISTANCE
PLUMED: with label COMdist
PLUMED: between atoms 53576 53577
PLUMED: using periodic boundary conditions
PLUMED: Action DISTANCE
PLUMED: with label d1
PLUMED: between atoms 214 367
PLUMED: using periodic boundary conditions
PLUMED: Action DISTANCE
PLUMED: with label d2
PLUMED: between atoms 938 785
PLUMED: using periodic boundary conditions
PLUMED: Action UPPER_WALLS
PLUMED: with label COMuwall
PLUMED: with stride 1
PLUMED: with arguments COMdist
PLUMED: at 2.500000
PLUMED: with an offset 0.000000
PLUMED: with force constant 1000.000000
PLUMED: and exponent 2.000000
PLUMED: rescaled 1.000000
PLUMED: added component to this action: COMuwall.bias
PLUMED: added component to this action: COMuwall.force2
PLUMED: Action LOWER_WALLS
PLUMED: with label COMlwall
PLUMED: with stride 1
PLUMED: with arguments COMdist
PLUMED: at 1.380000
PLUMED: with an offset 0.000000
PLUMED: with force constant 1000.000000
PLUMED: and exponent 2.000000
PLUMED: rescaled 1.000000
PLUMED: added component to this action: COMlwall.bias
PLUMED: added component to this action: COMlwall.force2
PLUMED: Action UPPER_WALLS
PLUMED: with label d1uwall
PLUMED: with stride 1
PLUMED: with arguments d1
PLUMED: at 1.260000
PLUMED: with an offset 0.000000
PLUMED: with force constant 1000.000000
PLUMED: and exponent 2.000000
PLUMED: rescaled 1.000000
PLUMED: added component to this action: d1uwall.bias
PLUMED: added component to this action: d1uwall.force2
PLUMED: Action LOWER_WALLS
PLUMED: with label d1lwall
PLUMED: with stride 1
PLUMED: with arguments d1
PLUMED: at 1.228000
PLUMED: with an offset 0.000000
PLUMED: with force constant 1000.000000
PLUMED: and exponent 2.000000
PLUMED: rescaled 1.000000
PLUMED: added component to this action: d1lwall.bias
PLUMED: added component to this action: d1lwall.force2
PLUMED: Action UPPER_WALLS
PLUMED: with label d2uwall
PLUMED: with stride 1
PLUMED: with arguments d2
PLUMED: at 1.228000
PLUMED: with an offset 0.000000
PLUMED: with force constant 1000.000000
PLUMED: and exponent 2.000000
PLUMED: rescaled 1.000000
PLUMED: added component to this action: d2uwall.bias
PLUMED: added component to this action: d2uwall.force2
PLUMED: Action LOWER_WALLS
PLUMED: with label d2lwall
PLUMED: with stride 1
PLUMED: with arguments d2
PLUMED: at 1.196000
PLUMED: with an offset 0.000000
PLUMED: with force constant 1000.000000
PLUMED: and exponent 2.000000
PLUMED: rescaled 1.000000
PLUMED: added component to this action: d2lwall.bias
PLUMED: added component to this action: d2lwall.force2
PLUMED: Action METAD
PLUMED: with label metad
PLUMED: with stride 1
PLUMED: with arguments phi psi COMdist d1 d2
PLUMED: The number of bins will be estimated from GRID_SPACING
PLUMED: Gaussian width 0.060000 0.060000 0.060000 0.060000 0.060000
Gaussian height 0.200000
PLUMED: Gaussian deposition pace 1
PLUMED: Gaussian file HILLS_neu_mut_meta_A
PLUMED: Well-Tempered Bias Factor 10.000000
PLUMED: Hills relaxation time (tau) 0.231973
PLUMED: KbT 2.577483
PLUMED: Grid min -pi -pi 0 0 0
PLUMED: Grid max pi pi 2.5 2.5 2.5
PLUMED: Grid bin 629 629 251 251 251
PLUMED: Grid uses spline interpolation
PLUMED: added component to this action: metad.bias
PLUMED: added component to this action: metad.work
Many thanks
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
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