BTW,
I strongly suggest not simply use CHARMM-GUI for the membrane system
building since there are so many atom clashes and steric problem from
CHARMM GUI output which is completely unacceptable for MD simulations,
otherwise we probably waste tens of ns for the equilibration step. Even the
author of CHARMM GUI deny this issue at recent CHARMM workshop. I test such
system with crystal structures and the helix moved even so much at initial
few ns simulation which should be expected at micro second time scale......
I strongly suggest Amber develop its own membrane building tools
introducing OPM position. As far as I know three different membrane system
building methods based on pre-equilibrated membranes are available in
Gromacs and each of them works much much better than CHARMM-GUI.
2012/6/7 Ross Walker <ross.rosswalker.co.uk>
> Hi Albert,
>
> Thanks for the interest.
>
> This workshop should not actually be advertised yet. We are still in the
> process of determining who will be involved, what the program will be etc.
> Hence what is posted on the CECAM website (by CECAM, not us) for this is
> just a placeholder. We will be finalizing the program and advertising the
> workshop proper in a few months. We'll take it into account to try to
> include some examples on building and simulating membranes. Thank you for
> the suggestion.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Albert [mailto:mailmd2011.gmail.com]
> > Sent: Thursday, June 07, 2012 10:07 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] up coming workshop?
> >
> > hello:
> >
> > I found a up coming Amber workshop would be held in Europe and I
> > found
> > that there is no membrane protein simulation in this event. In fact, it
> > is
> > almost the same with the one which hold in Shanghai last year. Could
> > someone from Amber could add membrane protein simulation in this event?
> >
> > THX
> > Albert
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Jun 08 2012 - 03:00:03 PDT
