[gmx-users] Martini CG water

Ming Tang m21.tang at qut.edu.au
Wed May 13 03:53:15 CEST 2015

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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