Re: Simulating SDS molecules

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jun 30 2017 - 09:20:08 CDT

Hi,

Unless you have a super-super-super-duper computer you will need to use a
coarse grained force field.
Martini is such a forcefield, which also has SDS allready parametrized
<http://cgmartini.nl/index.php/force-field-parameters/lipids/surfactants>.
I'm not sure how well the CMC of SDS will be reproduced, but it would be
interesting to find out. You should also conduct a thorough literature
search, to see what has already been done.

Best,
Ajasja

On 30 June 2017 at 16:11, 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
>
>
>

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