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

From: Fabian Glaser <>
Date: Mon, 8 Sep 2014 16:44:36 +0300

Dear Jason,

Another question to came to my mind while preparing the system. Actually I want to do three simulations, one with only DIR molecules, a second one with only DAR molecules and a third one with a mixture....

- So in the case in which I have a single type, should I choose one specific molecule and keep fixed? Or just after the simulation choose one and calculate RDF?

- Actually the same question is valid for the mixture...

- I am having some difficulties in preparing the system, how many molecules, how to choose their number and box size, etc., as I explained in my previous email.

I would really like to participate in an advance amber course, is there such a thing in Europe?

Also I am thinking on organizing one in Israel if if is possible.



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
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Mon Sep 08 2014 - 07:00:05 PDT
Custom Search