[gmx-users] martini issues
m21.tang at qut.edu.au
Wed May 13 04:21:07 CEST 2015
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.
More information about the gromacs.org_gmx-users