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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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