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

From: Jason Swails <>
Date: Mon, 08 Sep 2014 10:22:30 -0400

On Sun, 2014-09-07 at 15:05 +0300, Fabian Glaser wrote:
> Dear Jason,
> Thanks again, more questions, hope this is OK ....
> 1) If I understand correctly, what you suggest is to perform a
> simulation with explicit water, with a number of molecules at a
> certain fixed distance of a central molecule and compute the density
> distribution of all of them around the central molecule after
> simulation with RDF and PMF functions for the central molecule once
> the simulation is completed. Correct? Or you mean just to use a number
> of molecules in a box at the same distance between them?

No, not a fixed distance. Just a bunch of the molecules in a simulation
box that move freely. There is no "central" molecule (or alternatively,
every molecule is a "central" molecule surrounded by all of the others).
> 2) How to choose the distance to use between the central molecules and
> the other molecules to create the water box? The molecules are about
> 20 Ang long full extended, so I guess the box has to be about 50 Ang
> minimum, I could take a distance of 12 Ang for any molecule is that a
> good approach?

I was under the impression that the molecules were significantly
smaller. The whole RDF approach is unlikely to work with such a large
molecule (especially if it is not rigid). It is going to be difficult
to characterize the interactions between two large, flexible molecules
since there are many degrees of freedom dictating the nature of their
interactions (a simple distance is unlikely to give all the information
you need unless you can fully sample the equilibrium distributions of
their different conformational states -- akin to umbrella sampling).
> 3) How many molecules to add, I have no idea what the concentration
> should be in vivo? At which distance from the central molecule?

This sounds like information you would need to figure out as part of
your study. Since it's not my study, I don't know.
> 4) How long the simulation should be? Until know I did 20 ns
> simulations, but would that be enough to calculate the RDF function
> later?

In general, they should be long enough to converge your results. A
decent first check is to compute the properties you're trying to find
for separate chunks of your simulation and make sure that they are the
> 5) Is the parametrization with antechamber a reasonable one?

Depends on your molecule. For a flexible molecule that is ~20 A
extended, I would not rely on antechamber torsion profiles being


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 08 2014 - 07:30:03 PDT
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