[gmx-users] Error with MARTINI depending by the box size

Mark Abraham mark.j.abraham at gmail.com
Mon Dec 10 23:08:39 CET 2012

On Mon, Dec 10, 2012 at 9:48 PM, francesco oteri
<francesco.oteri at gmail.com>wrote:

> Dear gromacs users,
> I am facing a very tricky problem in building a stable topology.
> In particular I am trying to use MARTINI force-field and I noticed that if
> I use a box whose the side size is smaller than 20nm, the minimization
> fails with this message:
> Reading file 01em.tpr, VERSION 4.6-beta1 (single precision)
> Starting 12 tMPI threads
> Using 12 MPI threads
> Making 2D domain decomposition 4 x 3 x 1
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+03
> Number of steps = 2000
> Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063
> Energy minimization has stopped, but the forces havenot converged to the
> requested precision Fmax < 1000 (whichmay not be possible for your system).
> It stoppedbecause the algorithm tried to make a new step whose sizewas too
> small, or there was no change in the energy sincelast step. Either way, we
> regard the minimization asconverged to within the available machine
> precision,given your starting configuration and EM parameters.
> Double precision normally gives you higher accuracy, butthis is often not
> needed for preparing to run moleculardynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
> writing lowest energy coordinates.
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy = 4.4209897e+18
> Maximum force = inf on atom 39063
> Norm of force = inf
> gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)
> But, if I use a box bigger then 19.5nm the minimization, although with some
> LINCS warning, succeeded!

The standard advice here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up seems to apply,
because your system also has problems with 4.5.5 and even when it
"succeeds" there is evidence that something is not right (from the LINCS

> I found the problem with gromacs 4.5.5,  4.6beta1 and beta2.
> I am attaching the script (crea_topo.csh) I am using to build the
> topologies as well as all the input files you need to replicate the error.
> The different topologies have been obtained changing the value of the
> variable side in crea_topo.csh
> As you can notice from the script, the structure is initially minimized in
> vacuo to remove problems due in the all atoms-coarse grained transformation
> and then it is solvated, Then, water molecules closer then 0.8nm to protein
> are rmoved through vmd.
> Can you give me some clue on how to solve the problem, except changing the
> software?.

As the above link suggests, make sure you visualize your results. Probably
you will find an ion in an inappropriate place.

> I mean, I would like to know whether there is a bug or not in some of the
> program used to build the topology.

genion can insert ions of arbitrary name and update the topology in one
step. You don't need your second round of vmd or as much awking.

genbox can do similarly - I'm surprised there's not an existing Martini
workflow that uses genbox -vdwd 0.4 or similar to pre-exclude those waters.

Neither of these is likely your problem, however.


> Francesco
>  01em.mdp <
> https://docs.google.com/file/d/0B1ktZ-u2OHFAejUwY2tnQnlnc3c/edit>
>  crea_topo.csh<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAcHVZWXJCeXVBc3c/edit>
>  Desu_OK.pdb<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAMkRScXlWYWlzMmc/edit>
>  dsspcmbi <
> https://docs.google.com/file/d/0B1ktZ-u2OHFAT2hCWVpGWDAwdEU/edit>
>  ions.itp <
> https://docs.google.com/file/d/0B1ktZ-u2OHFAYWdpa3o3N09sdEU/edit>
>  martini.itp<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAOFVZNkwzN2J3c3c/edit>
>  martinize.py<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAZ3hzWnZGcEJyTWM/edit>
>  water-1bar-303K.gro<
> https://docs.google.com/file/d/0B1ktZ-u2OHFAcmhMUS1YZEVlUjQ/edit>
> --
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