[gmx-users] grompp/COM Pulling- Is number of pull groups an issue, an issue with the free energy of the molecule, or is there a limit to the size of the whole structure?

Shaun Tung shaun.tung at gmail.com
Thu Nov 16 19:17:30 CET 2017

I'm trying to grompp my files that has around 140 pull groups, but whenever
I try to pull more than 128 groups together, the grompp command stops

*Largest charge group radii for Van der Waals: 0.149, 0.149 nm*
*Largest charge group radii for Coulomb:       0.165, 0.164 nm*

and what is supposed to follow next is

*Pull group  natoms  pbc atom  distance at start  reference at t=0*

Here is a copy of the parameters I've been using in my .mdp file:

        pull-coordX-groups         = 1 2
        pull-coordX-k              = 500
        pull-coordX-init           = 0.150
        pull-coordX-type           = umbrella
        pull-coordX-geometry       = distance
        pull-coordX-dim            = Y Y Y
        pull-coordX-start          = no

where X ranges from 1-140. Some of the parameters are different as I'm
trying to pull 14 monomers together in a cylindrical pattern and some
groups will have different K values, but otherwise they are relatively the
same. After building my file with 140 pull groups and finding this error,
from the bottom of the page, I deleted out groups until the command ran
which was 128.

I then tried to evenly and manually take out groups in my file so that I
had 120 groups, but the command still failed.

When I ran with 10 monomers, grompp worked fine, and when I selected
manually the first ~11/14 monomers, grompp ran fine, but when I try to run
the whole structure, grompp seems to fail.

I am running without a PBC box.


        integrator               = md;steep
        tinit                    = 0
        dt                       = 0.0001
        ;emstep                   = 0.01
        comm_grps                = system

        ;          non-bonded
        rlist                    = 1.2
        coulombtype              = cut-off ;PME ;cut-off ;PME-switch
        rcoulomb-switch          = 1.15
        rcoulomb                 = 1.2
        pme_order                = 4
        optimize_fft             = yes
        vdwtype                  = cut-off
        rvdw-switch              = 1.15
        rvdw                     = 1.2
        DispCorr                 = no ;enerPres ;no ;enerPres
        ;ewald_rtol               = 1e-5

        comm_mode                = ANGULAR ;ANGULAR
        nsteps                   = 1000000
        nstxout                  = 10000;10000
        nstvout                  = 10000
        nstlog                   = 1000
        nstenergy                = 1000
        ;nstxtcout                = 10000
        ;xtc_grps                 = Protein
        energygrps               = System
        cutoff-scheme            = group ;verlet
        nstlist                  = 10
        ns_type                  = grid
        pbc                      = no
        nstcomm                  = 1000

Any help would be much appreciated! Thanks!


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