[gmx-users] Gromacs 2018 beta: g_membed broken?

Mark Abraham mark.j.abraham at gmail.com
Fri Dec 22 11:25:46 CET 2017


Hi,

Sounds like we might have made a bug in membed, which would be good to fix.
If you can file an issue at https://redmine.gromacs.org that would be
welcome.

Mark

On Wed, Dec 20, 2017, 5:43 AM Daniel Bauer <bauer at cbs.tu-darmstadt.de>
wrote:

> Hello,
>
> Im using g_membed to insert potassium channels into POPC membranes. My
> "standard protocol" which worked very well for me on all proteins I used
> so far seems to not work with gromacs 2018 (using the exact same input
> files).
>
>
> This is what I am doing:
>
> 1) orienting the protein onto the membrane (lambada)
>
> 2) Merging the topology files for the membrane and protein
>
> 3) grompp: gmx grompp -f g_membed.mdp -n -c input.gro -r input.gro -o
> g_membed.tpr --maxwarn 2
>
> 4) gmx mdrun -deffnm g_membed -membed embed.dat -mn index.ndx -mp
> embedded.top -c embedded.top # selecting protein and membrane group
>
>
> First thing I noticed is that the number of warnings i have to ignore
> during grompp increased by one because of the new PME warning for
> charged systems. My protein has a net charge, so I have to choose if i
> insert counter ions before or after protein insertion (and I chose to do
> it after insertion).
>
> So the warnings I get are:
>
> WARNING 1: You are using Ewald electrostatics in a system with net
> charge  // I think I can ignore this since I neutralize right after
> insertion.
>
> WARNING 2: Can not exclude the lattice Coulomb energy between energy
> groups // g_membed does not support verlet
>
>
> Finally when I run the insertion simulation on the 2018 beta I get the
> following error:
>
> step 0: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
> Wrote pdb files with previous and current coordinates
> step 0Warning: Only triclinic boxes with the first vector parallel to
> the x-axis and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={        -nan,         -nan,         -nan}
>             Box[    1]={        -nan,         -nan,         -nan}
>             Box[    2]={        -nan,         -nan,         -nan}
>          Can not fix pbc.
>
> This seems to happen independent of my system (I tried several of my
> membrane patches and proteins that worked previously). All of them
> insert into the membrane with 2016 successfully but fail on the 2018
> version. So far I tried to increase the number of steps, reduced the
> timestep and played arround with xyinit and zinit as well as setting
> -DFLEXIBLE in the mdp, but no success.
>
> Any idea whats wrong? Or should I move this issue directly to redmine
> since its related to a version update?
>
>
> This is my embed.dat file:
>
> nxy        = 1000
> xyinit        = 0.1
> xyend        = 1.0
> rad        = 0.22
> ndiff        = 0
> asymmetry    = no
> pieces        = 1
> maxwarn        = 1
>
>
> And my mdp:
>
> ; Run parameters
> integrator    = md
> nsteps        = 1000
> dt            = 0.002
>
> ; I have posres for the protein enabled, although this is irrelevant
> because the protein group coords are frozen. Same issue if i disable
> this and remove posres!
> refcoord_scaling = all
>
> ;define = -DFLEXIBLE ; does not help
>
> ; membed options
> energygrps    =    insertion_group
> freezegrps    =    insertion_group
> freezedim    =    Y Y Y
> energygrp_excl    =    insertion_group insertion_group
>
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 1000
> nstenergy                = 100
> nstxtcout                = 1000
>
> ; Bond parameters
> continuation    = no
> constraint_algorithm = lincs
> lincs_iter    = 2
> lincs_order    = 8
>
> ; CHARMM36 params
> constraints = h-bonds
> cutoff-scheme = Group        ; Verlet is not supported by g_membed
> vdwtype = Cut-off
> vdw-modifier = force-switch
> rlist = 1.2
> rvdw = 1.2
> rvdw-switch = 0.8
> coulombtype = PME
> rcoulomb = 1.2
> DispCorr = no
>
> ; Temperature coupling
> tcoupl        = V-rescale
> tc-grps        = Other Water_and_ions Protein
> tau_t        = 0.1    0.1 0.1
> ref-t =  298.0  298.0  298.0
>
>
> ; Pressure coupling
> pcoupl                  = Berendsen
> pcoupltype              = semiisotropic
> tau_p                   = 5.0
> compressibility         = 4.5e-5  4.5e-5
> ref_p                   = 1.0     1.0
>
>
> ; Periodic boundary conditions
> pbc            = xyz
>
>
> ; Velocity generation
> gen_vel        = yes
> gen_temp    = 298.0
> gen_seed    = -1
>
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> comm-mode    = Linear
> comm-grps    = Other Water_and_ions Protein
>
>
> Best regards,
>
> Daniel
>
>
> --
> Daniel Bauer, M.Sc.
>
> TU Darmstadt
> Computational Biology & Simulation
> Schnittspahnstr. 2
> 64287 Darmstadt
> bauer at cbs.tu-darmstadt.de
>
> Don't trust atoms, they make up everything.
>
> --
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