[gmx-users] Drude-2013 FF, seg fault 11 on repeat minimization of beta-D-glucose monomer

Dayhoff, Guy gdayhoff at health.usf.edu
Wed Feb 15 20:06:16 CET 2017


   Thanks for taking the time to humor my inquiry.

    I’m hoping to find a fix for my issue or obtain a working beta-D-glucose monomer model that I can use to
          continue troubleshooting my issue. Details below… (This is my first post, forgive me for including too much/
  too little context)

  My Best,
     Guy Dayhoff

   I am attempting to employ the Drude-2013FF available below to use with some carbohydrates:


   I have obtained and installed the DRUDE compatible GROMACS distro available via:

 git clone git://git.gromacs.org/gromacs.git
 cd gromacs
    git checkout drude

    I am using pre-equilibrated SWM4-NDP water available from:


    I have adjusted Drude parameters in my mdp files as demonstrated in the additional material from the publication
    regarding implementation of the Drude FF and extended Lagrangian dynamics in GROMACS.

     Publication: http://dx.doi.org/10.1002/jcc.23937

    drude = yes
     drude-mode = SCF
     drude-hyper = yes
     drude-khyp = 16736000.0
     drude-r = 0.02
     drude-pow = 4

    I prepared a Drude model of beta-D-glucose(BGLC) to run before using more complex models by:

Downloading .CIF and .SDF data from RCSB-PDB @ https://www3.rcsb.org/ligand/BGC

Feeding this data into the CHARMM-GUI’s Ligand Reader & Modeler to produce .PDB and .PSF files

Feeding the .PDB and .PSF files into the CHARMM-GUI’s Drude Prepper producing bDgluc-Drude.pdb

    I generated a topology file with pdb2gmx without any warnings/notes/errors:

gmx pdb2gmx -f bDgluc-Drude.pdb -o bDgluc-Drude.gro -p bDgluc-Drude.top

    I placed the BGLC model in the center of a 3.0 x 3.0 x 3.0 box and minimized successfully:

gmx editconf -f bDgluc-Drude.gro -o bDgluc-Drude-CEN.gro -box 3.0 3.0 3.0 -center 1.5 1.5 1.5

        gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-CEN.gro -p bDgluc-Drude.top -o bDgluc-Drude-EMV.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMV

    I then solvate the system and attempt to minimize it once more, this results in a seg fault 11:

gmx solvate -cp bDgluc-Drude-EMV.gro -cs swm4-ndp.gro -p bDgluc-Drude.top -o bDgluc-Drude-SOL.gro

        gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-SOL.gro -p bDgluc-Drude.top -o bDgluc-Drude-EMS.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMS

Step=    0, Dmax= 1.0e-02 nm, Epot=          nan Fmax= 3.77896e+06, atom= 16
Segmentation fault: 11

    Likewise, if I simply take the minimized BGLC and attempt to minimize a second time I get the seg fault 11:

        gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-EMV.gro -p bDgluc-Drude.top -o bDgluc-Drude-EMV2.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMV2

Step=    0, Dmax= 1.0e-03 nm, Epot=          nan Fmax= 1.95057e+04, atom= 11
Segmentation fault: 11

    I have attempted to isolate the cause and have noted:

      minimization and subsequent runs of a box of pure swm4-ndp produces no such errors, indicating the issue
is most likely related to the BGLC molecule in the system.

when beginning with a beta-D-glucose model not prepared with the CHARMM-GUI Drude Prepper (i.e. without
        lone pairs and drudes included in the coordinate file) pdb2gmx properly adds all drudes, however fails to add
        LP5A and LP5B, LPX5 is added though (CHARMM-GUI’s Drude Prepper doesn’t appear to have this issue).

        using the -missing flag and proceeding with minimzation, solvation, NVT and NPT ensembles using the incomplete
        model does not cause any seg faults and completes without errors.  In this case however, the molecule has a charge
        (which corresponds exactly to the missing LP5A and LP5B).

with all things considered, I believe the issue lies with the handling of LP5A/LP5B in the BGLC residue in my model
but am unsure of how to proceed at this point.

the seg fault: 11 occurs on the first step of the minimizations

     My complete min.mdp for reference:

define                   =

integrator                = steep
nsteps                    = 10000
dt                       = 0.001
comm-mode            = Linear
nstcomm                 = 1
nstcalcenergy = 1

ns-type                   = grid
rlist                        = 1.2
pbc                         = xyz
cutoff-scheme           = Verlet
periodic-molecules    = no

constraints  = none
continuation              = no

coulombtype              = PME
rcoulomb                = 1.2
vdwtype                     = Cut-off
rvdw                       = 1.2
DispCorr                    = EnerPres
vdw-modifier   = potential-switch
rvdw-switch               = 1.0

emtol                      = 10.0
emstep                   = 0.001

fourierspacing            = 0.1
pme_order                 = 4
ewald_rtol                 = 1e-5
ewald_geometry     = 3d

drude = yes
drude-mode = SCF
drude-hyper = yes
drude-khyp = 16736000.0
drude-r = 0.02
drude-pow = 4

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