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

From: Fabian Glaser <>
Date: Sun, 7 Sep 2014 15:05:23 +0300

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?

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?

3) How many molecules to add, I have no idea what the concentration should be in vivo? At which distance from the central molecule?

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?

5) Is the parametrization with antechamber a reasonable one?

6) Again this is completely new to me, so if you know about any publication that tries to do something similar, I would appreciate any pointer.

Thanks a lot !!

Fabian Glaser, PhD

Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU

The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
Tel: +972 4 8293701
Fax: +972 4 8225153

On Sep 4, 2014, at 2:55 PM, Jason Swails <> wrote:

> On Thu, Sep 4, 2014 at 7:37 AM, Fabian Glaser <>
> wrote:
>> Thanks a lot Jason,
>> Would it be possible that you send me an example of the RDF and PMF that I
>> could use as input to amber ?
>> Or a pointer to the relevant information / paper / examples ?
>> I would try to implement what you suggest but I don't have experience with
>> RDF or PMF.
> ​cpptraj computes the radial distribution function. A PMF is a potential
> of mean force -- basically the free energy along a reaction coordinate.
> Since the radial distribution function is, in essence, a probability
> function, the negative logarithm of the RDF _is_ the PMF.
> HTH,
> Jason
> ​
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Sep 07 2014 - 05:30:02 PDT
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