[gmx-users] Martini CG water

[João Henriques]

​This is duplicate. Check my answer to the other email.

/J​

On Wed, May 13, 2015 at 3:53 AM, Ming Tang <m21.tang at qut.edu.au> wrote:

> Dear all,
>
>
> I am trying to learn simulation in gromacs 5.0.4 using martini force
> field, when learning the tutorial (
> http://md.chem.rug.nl/cgmartini/index.php/proteins) step by step, I got
> the following note when doing gmx slovate:
>
> NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
> removed in a future release when 'verlet' supports all interaction forms.
>
>
> The CG water model ( water-box-CG_303K-1bar.gro) is downloaded from that
> tutorial website. I checked the 5.0.4 mannual, but found little information
> about Martini. could anybody tell me where to download the CG water model
> suitable for verlet? And what's the difference between Martini22 force
> field and Martini22p force field?
>
>  Besides, when solvating the model using "gmx solvate -cp
> minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o
> system-solvated.gro", I got the following warning:
>
>
> 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.
>
> I run gmx solvate -h, but still have no idea to fix this problem. I have
> set Van der Walls distance in the command. could anybody give me some
> guidance?
>
>
> Thanks in advance.
> --
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