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

From: Fabian Glaser <>
Date: Thu, 4 Sep 2014 14:37:13 +0300

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.

Best regards,


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 2:29 PM, Jason Swails <> wrote:

> On Thu, Sep 4, 2014 at 3:44 AM, Fabian Glaser <>
> wrote:
>> Hi Jason,
>> Thanks a lot for your quick answer, my objective is to study the
>> interaction between tow small molecules, but since I have no idea of how
>> they interact, what I thought is to use implicit solvent model and then
>> pull and push the molecules from each other slowly and keep 50 or 100
>> conformations when they are close, to start a long dynamics for each of
>> them. The idea is to obtain the largest possible sampling, without
>> investing 3 months.The problem with the umbrella sampling (which I may not
>> to understand correctly) is that I don't even know what is the appropriate
>> distance between center of masses of both molecules, or when I should stop
>> the simulation.
> ‚ÄčI wasn't suggesting actually doing umbrella sampling. I was suggesting
> that you sample at fixed distances rather than do the constant
> pushing/pulling. I believe that sampling at fixed distances will be a
> better approach (it won't take as long and it'll give you more, better
> starting spots at different distances for longer simulations).
> However, I don't think that your approach is likely to yield interesting
> results. Small molecules that are actually soluble rarely interact
> strongly enough to stay close to each other under the conditions of
> infinite dilution (and an implicit solvent simulation is infinitely
> dilute). You are probably more likely to extract meaningful interaction
> profiles by loading a solvent box with a handful of these compounds and
> computing radial distribution functions (RDF). These are directly related
> to the PMF along the RDF coordinate (namely, the distance between the two
> species). The free energy obviously has a concentration dependence to it,
> but you will know what that concentration is.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Sep 04 2014 - 05:00:06 PDT
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