Simulating protein-membrane systems in implicit solvent is a complicated
task and I don't think there are thoroughly tested protocols to do that in
AMBER or any other popular MD engine. I know CHARMM supports implicit
solvent - implicit membrane simulations, although with some known
inaccuracies.
Thomas
On 18 January 2013 11:07, HM <scienceamber.gmail.com> wrote:
> Thank Ross,
> I am new to Umbrella Sampling, It would be nice if I will get some help
> from a nice tutorial. I searched but could not find a good one.
> I have a query regarding the system complexity. Since I have limited
> processors to run the job, shall I try Umbrella Sampling in implicit
> solvent, will the results reliable?
>
> Thanks,
>
> On Fri, Jan 18, 2013 at 9:38 AM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > would take a good look in the literature at what people do in these
> > situations. The issue with your 'control' is that you make no mention of
> > timescale. The experimental data may indeed show that the peptide
> > penetrates the membrane but does it give any indication of the timescale
> > that this takes? If it is on the order of milliseconds then just running
> > brute force MD is not going to work. One option would be to try some form
> > of umbrella
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 18 2013 - 07:30:02 PST
