Re: [AMBER] many initial systems for a two molecules system

From: Jason Swails <>
Date: Mon, 08 Sep 2014 10:58:44 -0400

On Mon, 2014-09-08 at 17:35 +0300, Fabian Glaser wrote:
> Oh I see, I thought to use the center of mass starting from a PDB
> structure....yes they are big molecules
> Their flexibility is not so large since they have 3-4 aromatic rings,
> so you say I cannot use the RDF approach without previously
> equilibrating the system seriously?

If they're not so flexible you may still be able run a simulation with a
box of the molecules and use the RDF to get some idea of their
> Well, my original idea was to gain some insight at all about their
> interaction, couldn't I first run a single molecule and then freeze
> the best 5 conformations to calculate RDF?

I was talking about inter-molecular RDFs. That obviously won't work
with only a single molecule. In any case, it was just an idea (that may
amount to nothing) to help get you started.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 08 2014 - 08:00:03 PDT
Custom Search