[gmx-users] GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

Hello Albert,

Thanks.
Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5
provides only the option for CHARMM27 FF and I found that ff43a1 very well
preserves the characters of both the protein as well as the lipids for
fairly long simulation time, hence I used that FF in the tutorial. But one
can surely add CHARMM36 to GROAMCS by doing all the necessary topology
conversions.


Regards,

Anirban

On Thu, Apr 26, 2012 at 3:08 PM, Albert <mailmd2011 at gmail.com> wrote:

>  it seesm to be good.
> just one pieces of advices, why not use CHARMM36 for this tutorial ? since
> it is the best FF for lipids currently.
>
>
> On 04/26/2012 11:14 AM, Anirban Ghosh wrote:
>
> Hi ALL,
>
>  I have prepared a step-wise tutorial for running a MD simulation of a
> GPCR protein inserted in a lipid bilayer. It can be found at the following
> URL:
>
>  https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>
>  I sincerely hope it will help people who are new to such simulations and
> the GROMACS community in general. This tutorial is adapted from the
> membrane protein tutorial prepared by Justin Lemkul.
>
>
>  Regards,
>
>  Anirban
>
>
>
>
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