[gmx-users] martini issues

[Ming Tang]

Dear Joao and Tsjerk,

Thanks for your answer and guidance.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, 13 May 2015 7:34 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] martini issues

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 definite :)

Cheers,

Tsjerk

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,
> João
>
>
> 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
> solvate
> > -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
> > 0.21
> -o
> > system-solvated.gro.
> >
> >
> > WARNING: Masses and atomic (Van der Waals) radii will be guessed  
> > based
> on
> > residue and atom names, since they could not be definitively 
> > assigned
> from
> > 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
> about
> > martini. hope to receive guidance about this.
> >
> >
> > thanks in advance.
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--
Tsjerk A. Wassenaar, Ph.D.
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