[gmx-users] Minimum periodic distance
Mark.Abraham at anu.edu.au
Sat May 28 09:58:36 CEST 2011
On 28/05/2011 2:16 PM, Kavyashree M wrote:
> Dear users,
> I ran a simulation of a protein in water with rlist = rcoloumb = 1.4nm,
> rvdw = 1.0nm, with PME and the distance between in the periodic
> was set to a minimum of 2.0 i.,e distance between protein and cell
> edge was set to 1.0nm, Even then, when I ran g_mindist, there was
> a message stating that -
> "shortest periodic distance is 1.39714 (nm) at time 21824 (ps),
> between atoms 2062 and 3688"
> where 2062 is a protein atom and 21824 is a water molecule.
> I wanted to know why this happens in spite of taking care of it
Apparently you didn't achieve what you thought you achieved. Without
knowing what you did, nobody can say why, unless your protein unfolded.
Run g_mindist on your input structure to grompp.
> what are the consequences, what is the solution?
Maybe you didn't set up as large a box as you thought (read
documentation carefully for diameter-vs-radius effects), maybe your
simulation conditions are not stable for your protein, maybe you've run
a simulation that is flawed because the periodic images could see each
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