[gmx-users] Reg: Energy minimisation of hexane
mark.abraham at anu.edu.au
Wed Oct 6 08:47:56 CEST 2010
----- Original Message -----
From: vinothkumar mohanakrishnan <kmvinoth at gmail.com>
Date: Wednesday, October 6, 2010 17:18
Subject: Re: [gmx-users] Reg: Energy minimisation of hexane
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Hi Mark
> I saw both the .gro file of hexane before and after EM in VMD as well checked their coordinates. I am not able to make anything out of it. it will better if one knows how to find the steric clash between two molecules?.
It's best avoided rather than searched for. Consider whether your box size is suitable for your coordinates. Construct a simpler version that is easier to check by hand.
VMD is a good tool for seeking steric clashes, because its bond-creating heuristics when you load in a .gro file will normally indicate where atoms are too close together. From VMD's Tk console you can use "pbc box" to view the box wrt the coordinates.
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