[gmx-users] martini issues
tsjerkw at gmail.com
Wed May 13 11:33:47 CEST 2015
There's nothing to add to a perfect answer! Indeed 'p' is for 'polarizable'
and should be used with a polarizable water model (PW) and not with the
normal model (W). Also, Martini is not Gromacs, so information about the
force field should not be expected in the Gromacs manual, but can be found
in the papers describing Martini and on cgmartini.nl.
Please also note that I'm not an expert on the force field and its
parameterization. I wouldn't want my answers on that being considered
On Wed, May 13, 2015 at 9:22 AM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:
> Dear Ming,
> There is nothing to fix. The first note is a simple reminder that
> cutoff-scheme is deprecated. The second warning is what it is, a warning.
> The [ atomtypes ] in the martini ff do not specify the radii. However there
> are [ nonbond_params ] for the W atomtype, i.e. P4. The radius is
> implicitly included in these c6 and c12 parameters. This mismatch between [
> atomtypes ] and [ nonbond_params ] is what is raising the warning, but
> there's nothing to worry about. It's just how the ff was implemented.
> The ff with suffix 'p' is for use with the polarizable water model, if I'm
> not mistaken.
> To end, these are my 50 cents on the subject. I may be wrong, which would
> not be the first time :) Tsjerk will have the definite answer since he's
> directly involved in the project.
> Best regards,
> On Wed, May 13, 2015 at 4:05 AM, Ming Tang <m21.tang at qut.edu.au> wrote:
> > Dear all,
> > I am learning martini method in gromacs through the tutorial
> > http://md.chem.rug.nl/cgmartini/index.php/proteins.<
> > http://md.chem.rug.nl/cgmartini/index.php/proteins> when solvating the
> > system, I came across the following note:
> > NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
> > removed in a future release when 'verlet' supports all interaction forms.
> > right now, i am using water-box-CG_301K-1bar.gro, which I downloaded from
> > that tutorial website. could anybody tell me where i can get the CG water
> > model suitable for verlet cutoff-scheme?
> > Aslo, I got the following warning when doing gmx solvate using gmx
> > -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21
> > system-solvated.gro.
> > WARNING: Masses and atomic (Van der Waals) radii will be guessed based
> > residue and atom names, since they could not be definitively assigned
> > the information in your input
> > files. These guessed numbers might deviate from the mass and
> > radius of the atom type. Please check the output files if necessary.
> > could anybody tell me how to fix this? I run gmx solvate -h, but still
> > have no idea.
> > Besides, I am confused about the difference between the martini22 ff and
> > martini22p ff. when checking 5.0.4 manual, i found little information
> > martini. hope to receive guidance about this.
> > thanks in advance.
> > --
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Tsjerk A. Wassenaar, Ph.D.
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