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

From: Fabian Glaser <>
Date: Thu, 4 Sep 2014 10:44:45 +0300

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.

Well I guess I ned to try, any additional suggestions?

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 3, 2014, at 6:07 PM, Jason Swails <> wrote:

> On Wed, 2014-09-03 at 14:26 +0300, Fabian Glaser wrote:
>> Hi,
>> I would be grateful to get ideas or a sample script that does the
>> following: I would like to create many initial systems as possible for
>> two small molecules which are supposed to interact, including two
>> small molecules, in the following manner:
>> To start with the two molecules far away from each other (let's say
>> 50 Angs). Start pulling them to each other slowly (let's say 1
>> Angstrom in each 100 ps) until the final distance is 10 or 15
>> Angstroms. Once this distance is reached, to pull them apart to 50
>> Angstroms again, and continue doing this 50 times. In this way I would
>> like to get 50 initial structures where the two molecules are in close
>> contact. Then, I will perform 50 independent MD with these initial
>> conformations.
> You can do this using steered molecular dynamics if you wanted to (see
> chapter 23 of the Amber 14 manual regarding NMR restraint -- in
> particular the "jar" keyword). An example steered MD run (inspired by
> the Jarzynski equation) can be found in $AMBERHOME/test/jar.
> However, this seems like overkill just to get starting configurations.
> Why not just do a single steered MD scan and take conformations along
> the path? If you need more at a particular distance, you can run a
> short MD simulation with the restraint fixed at that distance (like
> umbrella sampling) and take multiple configurations that way.
> Also, if you plan on using explicit solvent, a 50 A separation can be
> challenging to _actually_ implement. Your box would have to be at least
> 100 A to maintain at least 50 A separation between all periodic images.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Sep 04 2014 - 01:00:02 PDT
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