Line minimizer aborted: step at upper bound ... FATAL: allocation failure in vector()

[Xiaowen Wang]

I utilized version 1.6.2 of gmx_MMPBSA for conducting normal mode analysis. However, the analysis encountered an error: "Line minimizer aborted: step at upper bound ... FATAL: allocation failure in vector()." The trajectory was thoroughly checked for consistency. Below, you'll find the parameter settings and output information associated with this issue.

mmpbsa.in:

&general
sys_name="NMode",
startframe=1,
endframe=1000,
forcefields="leaprc.protein.ff14SB,leaprc.gaff"
PBRadii=2,
/
&nmode
nmstartframe=1,
nmendframe=1000,
nminterval=40,
/

output information:

WARNING: No ICDs were found. Either,
- Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or
- Make your system-wide implementation visible by installing ocl-icd-system conda package.
[INFO   ] Starting gmx_MMPBSA v1.6.2
[INFO   ] Command-line
  mpirun -np 8 gmx_MMPBSA -O -i /home/xwpnp/Tools/mdp-mmpbsa-gaff-input-files/gmxMMPBSA/mmpbsa-nmode.in -cs ../md.tpr -ci ../index.ndx -cg 1 13 -ct ../md_pbsa.xtc -lm ../ligand.mol2 -o MMPBSA_BFE_nmode.dat -eo MMPBSA_BFE_nmode.csv

[INFO   ] Checking /home/xwpnp/Tools/mdp-mmpbsa-gaff-input-files/gmxMMPBSA/mmpbsa-nmode.in input file...
[INFO   ] Checking /home/xwpnp/Tools/mdp-mmpbsa-gaff-input-files/gmxMMPBSA/mmpbsa-nmode.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/xwpnp/Tools/software/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/xwpnp/Tools/software/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/xwpnp/Tools/software/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/xwpnp/Tools/software/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] mmpbsa_py_nabnmode found! Using /home/xwpnp/Tools/software/miniconda3/envs/gmxMMPBSA/bin/mmpbsa_py_nabnmode
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/xwpnp/Tools/software/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group Protein_MOL (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] Generating ligand parameters from ../ligand.mol2 file...
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group MOL (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Generating AMBER Compatible PDB Files...
[INFO   ] Changing the Complex residues name format from GROMACS to AMBER...
[INFO   ] Changing the Receptor residues name format from GROMACS to AMBER...
[INFO   ] Changing the Ligand residues name format from GROMACS to AMBER...
[INFO   ] Splitting  receptor and ligand in PDB files..
[INFO   ] Building tleap input files...
[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

tets

[INFO   ] 1000 frames were processed by cpptraj for use in calculation.
[INFO   ] 25 frames were processed by cpptraj for nmode calculations.
[INFO   ] Starting calculations in 8 CPUs...
[WARNING] PB/RISM/NMODE will be calculated with multiple threads, make sure you have enough RAM.
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning nmode calculations with /home/xwpnp/Tools/software/miniconda3/envs/gmxMMPBSA/bin/mmpbsa_py_nabnmode
[INFO   ]   calculating complex contribution...

              0%|          | 0/25 [elapsed: 00:00 remaining: ?]Line minimizer aborted: step at upper bound      0.088747963
Line minimizer aborted: step at upper bound      0.026557884
Line minimizer aborted: step at upper bound      0.058516659
Line minimizer aborted: step at upper bound      0.078145763
Line minimizer aborted: step at upper bound      0.078883414
Line minimizer aborted: step at upper bound      0.069065355
Line minimizer aborted: step at upper bound      0.061399551
Line minimizer aborted: step at upper bound      0.052118255
Line minimizer aborted: step at upper bound       0.04301772
Line minimizer aborted: step at upper bound      0.060771658
Line minimizer aborted: step at upper bound      0.060808227
Line minimizer aborted: step at upper bound      0.048505913
Line minimizer aborted: step at upper bound      0.038447661
Line minimizer aborted: step at upper bound      0.067116899
Line minimizer aborted: step at upper bound       0.05353654
Line minimizer aborted: step at upper bound      0.071241998
Line minimizer aborted: step at upper bound      0.071048002
Line minimizer aborted: step at upper bound      0.073593232
Line minimizer aborted: step at upper bound      0.084683461
Line minimizer aborted: step at upper bound      0.062137905
Line minimizer aborted: step at upper bound      0.083911307
Line minimizer aborted: step at upper bound      0.069525027
Line minimizer aborted: step at upper bound      0.020445261
Line minimizer aborted: step at upper bound      0.075686566
Line minimizer aborted: step at upper bound     0.0023277449
Line minimizer aborted: step at upper bound      0.080604972
Line minimizer aborted: step at upper bound    0.00018813699
Line minimizer aborted: step at upper bound    0.00031707566
Line minimizer aborted: step at upper bound     0.0021722215
Line minimizer aborted: step at upper bound     0.0074077259
Line minimizer aborted: step at upper bound      0.017161411
Line minimizer aborted: step at upper bound     0.0022166235
Line minimizer aborted: step at upper bound       0.02196892
Line minimizer aborted: step at upper bound      0.077510808
Line minimizer aborted: step at upper bound      0.035222911
Line minimizer aborted: step at upper bound      0.067025062
Line minimizer aborted: step at upper bound      0.047529754
Line minimizer aborted: step at upper bound    0.00098783711
Line minimizer aborted: step at upper bound      0.078022906
Line minimizer aborted: step at upper bound      0.079536358
Line minimizer aborted: step at upper bound    0.00071252439
Line minimizer aborted: step at upper bound       0.07628712
Line minimizer aborted: step at upper bound     0.0011215821
Line minimizer aborted: step at upper bound     0.0031749369
Line minimizer aborted: step at upper bound     0.0012692881
Line minimizer aborted: step at upper bound      0.023919956
Line minimizer aborted: step at upper bound     0.0037112421
Line minimizer aborted: step at upper bound      0.090815544
Line minimizer aborted: step at upper bound      0.066202264
Line minimizer aborted: step at upper bound     0.0028899277
Line minimizer aborted: step at upper bound     0.0031335969
Line minimizer aborted: step at upper bound      0.044038649
Line minimizer aborted: step at upper bound      0.028026631
Line minimizer aborted: step at upper bound      0.062537731
Line minimizer aborted: step at upper bound      0.025597497
Line minimizer aborted: step at upper bound    0.00054048917
Line minimizer aborted: step at upper bound       0.00212885
Line minimizer aborted: step at upper bound      0.070395284
Line minimizer aborted: step at upper bound     0.0013125421
Line minimizer aborted: step at upper bound     0.0024858576
Line minimizer aborted: step at upper bound     0.0032356501
Line minimizer aborted: step at upper bound      0.043337439
Line minimizer aborted: step at upper bound      0.028885601
Line minimizer aborted: step at upper bound      0.066823804
Line minimizer aborted: step at upper bound     0.0020238984
Line minimizer aborted: step at upper bound      0.069006882
Line minimizer aborted: step at upper bound     0.0058962136
Line minimizer aborted: step at upper bound    0.00024983627
Line minimizer aborted: step at upper bound      0.032442357
Line minimizer aborted: step at upper bound     0.0002857477
Line minimizer aborted: step at upper bound      0.022230453
Line minimizer aborted: step at upper bound    0.00015390333
Line minimizer aborted: step at upper bound     0.0063884619
Line minimizer aborted: step at upper bound    0.00010578982
Line minimizer aborted: step at upper bound     0.0036943062
Line minimizer aborted: step at upper bound     0.0056152035
Line minimizer aborted: step at upper bound      0.085891076
Line minimizer aborted: step at upper bound      0.045969896
Line minimizer aborted: step at upper bound     0.0024837486
Line minimizer aborted: step at upper bound     0.0016431601
Line minimizer aborted: step at upper bound      0.022921883
Line minimizer aborted: step at upper bound     0.0031519518
Line minimizer aborted: step at upper bound      0.014612796
Line minimizer aborted: step at upper bound     0.0010183213
Line minimizer aborted: step at upper bound      0.047944557
Line minimizer aborted: step at upper bound     0.0064542303
Line minimizer aborted: step at upper bound    2.7936739e-06
Line minimizer aborted: step at upper bound      0.026303181
Line minimizer aborted: step at upper bound     0.0037385323
Line minimizer aborted: step at upper bound     0.0064487242
Line minimizer aborted: step at upper bound       0.02122918
Line minimizer aborted: step at upper bound     0.0090868928
Line minimizer aborted: step at upper bound    0.00045560333
Line minimizer aborted: step at upper bound     0.0030129928
Line minimizer aborted: step at upper bound    3.5625676e-05
Line minimizer aborted: step at upper bound      0.012476294
Line minimizer aborted: step at upper bound      0.072911861
Line minimizer aborted: step at upper bound     0.0017671442
Line minimizer aborted: step at upper bound      0.017123338
Line minimizer aborted: step at upper bound      0.080513725
Line minimizer aborted: step at upper bound     0.0009867975
Line minimizer aborted: step at upper bound     0.0012831534
Line minimizer aborted: step at upper bound      0.013546283
Line minimizer aborted: step at upper bound      0.061551934
Line minimizer aborted: step at upper bound    0.00050285835
Line minimizer aborted: step at upper bound      0.036359473
Line minimizer aborted: step at upper bound     0.0087254952
Line minimizer aborted: step at upper bound      0.045068099
Line minimizer aborted: step at upper bound    0.00020503168
Line minimizer aborted: step at upper bound      0.034096851
Line minimizer aborted: step at upper bound      0.068457194
Line minimizer aborted: step at upper bound      0.061746702
Line minimizer aborted: step at upper bound      0.021074734
Line minimizer aborted: step at upper bound    0.00057667299
Line minimizer aborted: step at upper bound      0.010508177
Line minimizer aborted: step at upper bound      0.028626571
Line minimizer aborted: step at upper bound      0.024099321
Line minimizer aborted: step at upper bound      0.036755867
Line minimizer aborted: step at upper bound    0.00054255493
Line minimizer aborted: step at upper bound    0.00052428047
Line minimizer aborted: step at upper bound      0.081391058
Line minimizer aborted: step at upper bound     0.0012748798
Line minimizer aborted: step at upper bound     0.0003184994
Line minimizer aborted: step at upper bound     0.0036062025
Line minimizer aborted: step at upper bound    0.00021685991
Line minimizer aborted: step at upper bound     0.0002226229
Line minimizer aborted: step at upper bound    0.00015810426
Line minimizer aborted: step at upper bound      0.014318802
Line minimizer aborted: step at upper bound     0.0024631907
Line minimizer aborted: step at upper bound      0.025136876
Line minimizer aborted: step at upper bound      0.079263627
Line minimizer aborted: step at upper bound    0.00055908785
Line minimizer aborted: step at upper bound      0.019096906
Line minimizer aborted: step at upper bound     0.0029459636
Line minimizer aborted: step at upper bound       0.02848838
Line minimizer aborted: step at upper bound     0.0034069756
Line minimizer aborted: step at upper bound     0.0013283102
Line minimizer aborted: step at upper bound     0.0017605855
Line minimizer aborted: step at upper bound      0.011906459
Line minimizer aborted: step at upper bound     0.0086367225
Line minimizer aborted: step at upper bound      0.010479318
Line minimizer aborted: step at upper bound     0.0016084227
Line minimizer aborted: step at upper bound       0.12059365
Line minimizer aborted: step at upper bound      0.025156284
Line minimizer aborted: step at upper bound      0.069106626
Line minimizer aborted: step at upper bound    0.00072380712
Line minimizer aborted: step at upper bound      0.003752013
Line minimizer aborted: step at upper bound     0.0036615931
Line minimizer aborted: step at upper bound      0.043880058
Line minimizer aborted: step at upper bound       0.08256084
Line minimizer aborted: step at upper bound      0.062481778
Line minimizer aborted: step at upper bound    0.00078725462
Line minimizer aborted: step at upper bound    6.2569657e-05
Line minimizer aborted: step at upper bound      0.035432765
Line minimizer aborted: step at upper bound    0.00044573552
Line minimizer aborted: step at upper bound        0.5235958
Line minimizer aborted: step at upper bound     0.0010064477
Line minimizer aborted: step at upper bound      0.041054214
Line minimizer aborted: step at upper bound       0.07209871
Line minimizer aborted: step at upper bound     0.0010108831
Line minimizer aborted: step at upper bound    9.8039154e-05
Line minimizer aborted: step at upper bound       0.13388623
Line minimizer aborted: step at upper bound      0.027898217
Line minimizer aborted: step at upper bound     0.0037223109
Line minimizer aborted: step at upper bound    0.00095049142
Line minimizer aborted: step at upper bound      0.066076449
Line minimizer aborted: step at upper bound    0.00044703223
Line minimizer aborted: step at upper bound     0.0026552278
Line minimizer aborted: step at upper bound    0.00036424629
Line minimizer aborted: step at upper bound    0.00021085968
Line minimizer aborted: step at upper bound     0.0094496007
FATAL: allocation failure in vector()

[gmx_MMPBSA]

From this thread: http://archive.ambermd.org/201208/0124.html

The errors you're getting suggest a lack of memory. Nmode calculations
require storing a 3Nx3N Hessian matrix (although only an upper-triangular
portion is saved), as well as substantial scratch space for the work the
diagonalize has to do. When you run 8 threads that all happen to be
diagonalizing at the same time, that means you'll need 8x the amount of RAM
required for a single calculation.

Please, try with only one processor or increase the amount of memory. NMODE calculations tend to consume a lot of resources and take a long time, so be aware. I suggest go with a few frames first and do some testing before embarking in a long calculation