[gmx-users] Minimum periodic distance

Kavyashree M hmkvsri at gmail.com
Sat May 28 06:16:11 CEST 2011

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

what are the consequences, what is the solution?

Thanking you
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