Hi,
You could try starting with a standard solvated bilayer, then heating the system up to 1000K or so in NVT over 1ns (or longer, depending on your system size). This will give you a random mix of water and lipid.
Cheers,
Callum
PhD student
Imperial College London
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Lachele Foley (Lists)
Sent: 13 May 2012 02:49
To: AMBER Mailing List
Subject: Re: [AMBER] Placing molecules randomly in a simulation box
I'm unaware that the leaps have any built-in functions for randomization. But, it should be easy-ish to script. The "rand"
command will generate random numbers (e.g., "rand -N 10" outputs 10 random numbers... see "man rand"). Most programming languages also have some sort of internal randomization available. You can use those to add random transformations and/or translations (see manual) to your leap input files. The thing to make sure of is that each new random molecule isn't on top of another or in the middle of the protein, etc.
Depending on your needs, you might be able to do something simple-ish like a a minimum COM distance check to ensure that. You might want to let leap add the ions and waters after the POPE's so you have less to worry with in the script.
Of course, there might also be another utility for something like this.
On Sat, May 12, 2012 at 2:09 PM, Massimiliano Porrini <mozz76.gmail.com> wrote:
> Dear all,
>
> I need to randomly place ca. 200 molecules of the lipid POPE in my
> simulation box, and then create topology and coordinates files of the
> resulting system:
> protein + counter ions + POPE + water
>
> Is there any t/xleap procedure able to randomly place POPE molecules
> in the box (removing the potential clashing water)?
>
> Or I need to use another program?
> If so, can anyone suggest me which is the best solution?
>
> Thanks a lot in advance.
>
> Best,
>
>
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems School of Physics &
> Astronomy The University of Edinburgh James Clerk Maxwell Building The
> King's Buildings Mayfield Road Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon May 14 2012 - 03:30:03 PDT
