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

[Mark Abraham]

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
warnings)


> 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.

Mark


> 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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