[gmx-users] Forming a micelles

[Chih-Ying Lin]

Hi
I heard that it takes very long to see a micelle forming.
How long should be the simulation time to see the micelle forming?
How many nanoseconds to put on the simulation?


Is there any particular difference to simulate the micelles than other system?
My simulation steps are
1. prepare the topology files and coordinate files for the water and the solute
2. do the minimisation
3. generate the simulation box
4. put water and solute together
5. run MD with longer simulation time

Thank you
Lin

[Vitaly Chaban]

Post by Chih-Ying Lin
I heard that it takes very long to see a micelle forming.

I believe it's quite true.

Post by Chih-Ying Lin
How long should be the simulation time to see the micelle forming?
How many nanoseconds to put on the simulation?

I suggest you to use ngmx (or VMD) to monitor the trajectory and catch
the moment you are interested in.

[David van der Spoel]

Post by Chih-Ying Lin
Hi
I heard that it takes very long to see a micelle forming.
How long should be the simulation time to see the micelle forming?
How many nanoseconds to put on the simulation?
Is there any particular difference to simulate the micelles than other system?
My simulation steps are
1. prepare the topology files and coordinate files for the water and the solute
2. do the minimisation
3. generate the simulation box
4. put water and solute together
5. run MD with longer simulation time

@Article{ Marrink2000a,
author = "S. J. Marrink and D. P. Tieleman and A. E. Mark",
title = "Molecular dynamics simulation of the kinetics of
spontaneous micelle formation",
journal = "J Phys Chem B",
year = 2000,
volume = 104,
pages = "12165-12173"
}

Post by Chih-Ying Lin
Thank you
Lin
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[Arun kumar]

Hello there...
I carried out simulations of mixture of cationic
surfactants, fatty alcohols and water with various ratios of
surfactant/alcohol. Usually for a system of 100 surfactants +100
co-surfactants + 4000 water molecules, it took 3 x 600 ps to see the
micelles and other structures forming from random configurations.

Arun

On Tue, Sep 23, 2008 at 10:46 AM, David van der Spoel

Post by David van der Spoel

Post by Chih-Ying Lin
Hi
I heard that it takes very long to see a micelle forming.
How long should be the simulation time to see the micelle forming?
How many nanoseconds to put on the simulation?
Is there any particular difference to simulate the micelles than other system?
My simulation steps are
1. prepare the topology files and coordinate files for the water and the solute
2. do the minimisation
3. generate the simulation box
4. put water and solute together
5. run MD with longer simulation time

@Article{ Marrink2000a,
author = "S. J. Marrink and D. P. Tieleman and A. E. Mark",
title = "Molecular dynamics simulation of the kinetics of
spontaneous micelle formation",
journal = "J Phys Chem B",
year = 2000,
volume = 104,
pages = "12165-12173"
}

Post by Chih-Ying Lin
Thank you
Lin
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: [phone] fax: [phone]
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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[Chih-Ying Lin]

Hi
Would you please say more about your system?
How do you design / decide your simulation size of 100 surfactants +100
co-surfactants + 4000 water molecules??

How many surfactants will form a micelle?
How many atoms does one surfactant have?
How many atoms does one co-surfactant have?

Do you start from the critical micelle concentration?
You mentioned that it took 3 x 600 ps to see the micelles.
Do you mean that you have 3 computers to do the parallel simulation?

How long does it take to simulate 600 ps?
Do you visualize the whole 600 ps-image and SEE the micelle?
Or, other technique to KNOW the surfactants forming the micelles
without visualizing the system?

Thank you
Lin





Hello there...
I carried out simulations of mixture of cationic
surfactants, fatty alcohols and water with various ratios of
surfactant/alcohol. Usually for a system of 100 surfactants +100
co-surfactants + 4000 water molecules, it took 3 x 600 ps to see the
micelles and other structures forming from random configurations.

Arun

[Arun kumar]

Dear Lin,
Actually I chose the concentration randomly and viewed the
pictures. I used united atom force field. Surfactant is Behenyl trimethyl
ammonium chloride and co surfactant is stearyl alcohol. I did carry out
simulations for 4 different concentrations. I did not carry out simulations
to find out what is CMC.

For the system size I mentioned... I carried out simulations for 600 ps
from random configurations. And then I checked pictures and also checked
energies and other properties. And once again started from the final
configuration of the first simulation for next simulation (another 600 ps).
Similar way Third simulation.. In the last 600 ps I observed Micelle
formation and also energies and properties are constant over some 300 ps.

Only through visualization only I observed micelle formation.

With regards,
Arun

Post by Chih-Ying Lin
Hi
Would you please say more about your system?
How do you design / decide your simulation size of 100 surfactants +100
co-surfactants + 4000 water molecules??
How many surfactants will form a micelle?
How many atoms does one surfactant have?
How many atoms does one co-surfactant have?
Do you start from the critical micelle concentration?
You mentioned that it took 3 x 600 ps to see the micelles.
Do you mean that you have 3 computers to do the parallel simulation?
How long does it take to simulate 600 ps?
Do you visualize the whole 600 ps-image and SEE the micelle?
Or, other technique to KNOW the surfactants forming the micelles
without visualizing the system?
Thank you
Lin
Hello there...
I carried out simulations of mixture of cationic
surfactants, fatty alcohols and water with various ratios of
surfactant/alcohol. Usually for a system of 100 surfactants +100
co-surfactants + 4000 water molecules, it took 3 x 600 ps to see the
micelles and other structures forming from random configurations.
Arun

[hhhh huan]

Dear all,
I have read through the journal which David suggested. So,I am wonder how to generate the graph that show the comparison of the stability of cylindrical and sperical micell ( as stated as Figure 2 in that paper)

Thanks.

From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Forming a micelles
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Tuesday, September 23, 2008, 1:16 PM

Post by Chih-Ying Lin
Hi
I heard that it takes very long to see a micelle

forming.

Post by Chih-Ying Lin
How long should be the simulation time to see the

micelle forming?

Post by Chih-Ying Lin
How many nanoseconds to put on the simulation?
Is there any particular difference to simulate the

micelles than other system?

Post by Chih-Ying Lin
My simulation steps are
1. prepare the topology files and coordinate files for

the water and the solute

Post by Chih-Ying Lin
2. do the minimisation
3. generate the simulation box
4. put water and solute together
5. run MD with longer simulation time

@Article{ Marrink2000a,
author = "S. J. Marrink and D. P. Tieleman
and A. E. Mark",
title = "Molecular dynamics simulation of
the kinetics of
spontaneous micelle formation",
journal = "J Phys Chem B",
year = 2000,
volume = 104,
pages = "12165-12173"
}

Post by Chih-Ying Lin
Thank you
Lin
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at

http://www.gromacs.org/search before posting!

Post by Chih-Ying Lin
Please don't post (un)subscribe requests to the

list. Use the

Post by Chih-Ying Lin
www interface or send it to

gmx-users-request at gromacs.org.

Post by Chih-Ying Lin
Can't post? Read

http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular
Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: [phone] fax: [phone]
spoel at xray.bmc.uu.se spoel at gromacs.org
http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
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Please search the archive at http://www.gromacs.org/search
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Use the
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[Alif M Latif]

Date: Wed, 24 Sep 2008 10:15:44 -0700
From: "Chih-Ying Lin" <chihying2008 at gmail.com>
Subject: [gmx-users] Forming a micelles
To: arun.target at gmail.com
Cc: gmx-users at gromacs.org
??? <5777f3840809241015l2f0e85eo34dddc8f401864e1 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi
Would you please say more about your system?
How do you design / decide your simulation size of 100 surfactants +100
co-surfactants + 4000 water molecules??
How many surfactants will form a micelle?
How many atoms does one surfactant have?
How many atoms does one co-surfactant have?
Do you start from the critical micelle concentration?
You mentioned that it took 3 x 600 ps to see the micelles.
Do you mean that you have 3 computers to do the parallel simulation?
How long does it take to simulate 600 ps?
Do you visualize the whole 600 ps-image and SEE the micelle?
Or, other technique to KNOW the surfactants forming the micelles
without visualizing the system?
Thank you
Lin
******************************************

Dear Lin,
I have a suggestion:

Micelles should (theoretically) form above the CMC. So if you want a micelle, the concentration should be >>CMC
I suggest that you find the CMC experimentally, then convert the concentration to?nm^3 (let say: mv/1000nm^3)
The number of molecules should be able to obtained?by multiplying with Avogadro number: (6.023x10^23). If your system contain co-surfactant, then you'll need to get the experimetal CMC for at least one of the two surfactants.Take a look at this paper:
Bourov G. K. and Bhattacharya A., Brownian dynamics of mixed surfactant micelles, Journal of Chemical Physics, 123 (2005) 204712(1)-204712(6)
How long 600 ps simulation is depends on your system size,?box type, parameters and computational power (see manual).
One other way to KNOW the surfactants formed micelle is by measuring the surface tension (use g_energy). But g_energy gives surface*surface tension value, so you'll need to work on that. (HINT: Surface tension value drop drastically at CMC)

Hope these helps,

Muhammad Alif Mohammad Latif
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIA



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[Alif M Latif]

Dear Lin,
I have suggestions:

Micelles should (theoretically) form above the CMC. So if you want a micelle, the concentration should be >>CMC
I suggest that you find the CMC experimentally, then convert the concentration to?nm^3 (let say: mv/1000nm^3)
The number of molecules should be able to obtained?by multiplying with Avogadro number: (6.023x10^23). If your system contain co-surfactant, then you'll need to get the experimetal CMC for at least one of the two surfactants (if both non-ionic..if not you'll need the activity coefficient for each surfactant).Take a look at this paper:

Bourov G. K. and Bhattacharya A., Brownian dynamics of mixed surfactant micelles, Journal of Chemical Physics, 123 (2005) 204712(1)-204712(6)
How long 600 ps simulation is depends on your system size,?box type, parameters and computational power (see manual).
One other way to KNOW the surfactants formed micelle is by measuring the surface tension (use g_energy). But g_energy gives surface*surface tension value, so you'll need to work on that. (HINT: Surface tension value drop drastically at CMC)

Hope these helps,

Muhammad Alif Mohammad Latif
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIA



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[André Farias de Moura]

Post by Alif M Latif
One other way to KNOW the surfactants formed micelle is by measuring the
surface tension (use g_energy). But g_energy gives surface*surface tension
value, so you'll need to work on that. (HINT: Surface tension value drop
drastically at CMC)

the surface tension drop is due mainly to the presence of surfactant
molecules on the solvent surface. AFAIK all model systems representing
micellar solutions do not have any explicit interface, so it is
meaningless to calculate or analyze the surface tension.

Andr?

Post by Alif M Latif
Hope these helps,
Muhammad Alif Mohammad Latif
Department of Chemistry
Faculty of Science
Universiti Putra Malaysia
43400 UPM Serdang, Selangor
MALAYSIA
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&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&*&
Prof. Dr. Andr? Farias de Moura
Departamento de Qu?mica
Universidade Federal de S?o Carlos
S?o Carlos - SP - Brasil
tel. [phone]
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