[gmx-users] Martini CG water
joao.henriques.32353 at gmail.com
Wed May 13 09:23:23 CEST 2015
This is duplicate. Check my answer to the other email.
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
> Thanks in advance.
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