Re: Simulating SDS molecules

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jun 30 2017 - 09:27:36 CDT

Hi Siddharth, NAMD is the molecular dynamics engine, but the question also
depends on the choice of physical model, i.e. force field.

This calculation can be quite long and prohibitive for fully atomistic
force fields... For example, see this article where simulations were
carried out using a coarse-grained force field (that is much cheaper than
an atomistic model) and another MD software (HOOMD-Blue). The times
required to get statistically converged results were still fairly long:
http://pubs.rsc.org/en/content/articlehtml/2012/sm/c1sm06787g
Unfortunately the model used in the article uses a type of potential
(Shinoda et al, Mol Phys 2007) that is not supported in NAMD.

As far as I know, the only coarse-grained model well supported in NAMD is
MARTINI, because it was developed to reuse the same functions as atomistic
ones. But you may have more options with other programs used in
soft-matter simulations (e.g. HOOMD-Blue or LAMMPS).

NAMD excels particularly for simulations of biological macromolecules, or
in general systems that are well represented by the biological atomistic
force fields (CHARMM, AMBER, OPLS).

Giacomo

On Fri, Jun 30, 2017 at 10:11 AM, Siddharth Girdhar <
siddharth.gir47_at_gmail.com> wrote:

>
> Hi All,
>
>
>
> I am a highschool student who is trying to use NAMD for a research project
> I am doing. I wanted to find the critical micelle concentration (CMC) of
> Sodium Dodecyl Sulphate (SDS) in water by running a simulation on NAMD.
>
>
>
> I have followed the tutorials for NAMD and have a basic understanding of
> how it works. But most of it has been using proteins and I am unsure of how
> to work with surfactants like SDS. I have tried looking online but I havent
> found many resources for this.
>
>
>
> If anyone could point me in the right direction on how I can possibly find
> the CMC of SDS by running a simulation, that will be very appreciated.
>
>
>
> Thanks,
>
>
>
> Siddharth
>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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