Dear Dr. Ross,
Thank you for your advice. I just discussed this with my professor today,
and came up with a plan to work on it.
Slightly changed the protocol. But Im still eager to learn.
Thank you very much.
Regards,
Chinsu
On Wed, Sep 21, 2011 at 1:24 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > To start with, how big a box of water would it take to hold your
> > molecule in its extended shape?
> >
> > I set the water TIP3PBOX 12.0 and explicit solvent. Is it what you asked
> me
> > about? And when I visualize it in VMD, the water still scattered around
> the
> > protein (md11_water.png attached). Please correct me if i am wrong.
>
> Is that box big enough for your protein in its denatured state?
> The ideal would be a box sized for the fully-extended state in
> all dimensions.
>
> > What is your simulation rate for
> > problems of this size?
> >
> > I ran short minimization for the homology model, then heat it up (from 0K
> to
> > 400K) in 50ps to unfold the protein, and followed by a long MD in 300K to
> > re-fold it (expected in 100ns), but it is running still 60 ns. The
> protein
> > is 158 aa size.
>
> I was referring to your ns/day rate. E.g. if the rate of folding requires
> orders of magnitude more simulated time than you have grant money for,
> or career for that matter, it may not be a project that you want.
>
> Bill
>
> >
> > After taking some advice from Dr. Steinbrecher, I am pulling apart the
> > protein manually and run longer time for the heating process. Please
> advice
> > me more.
> >
> > I ran the process of MD (40ns) last time in 32 processors. It took 4
> days.
> > However, when I kept running another 40 ns, some errors were caused as it
> > said "related to some floating points", consequently the rst file wasn't
> > generated. We are trying to find out the reason for this issue in the
> mean
> > time, and I tried to run again the MD, and it is running still 60ns so
> far.
> >
> > Please advice me, and if possible, any more reading suggestions are also
> > appreciated.
> >
> > Thank you.
> >
> > Regards,
> > Chinsu
> >
> >
> >
> >
> >
> >
> > On Tue, Sep 20, 2011 at 11:36 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> > > > "Please consider that what you are trying to do is not a standard
> > > > simulation by any means, by prepared to invest lots of brain and
> computer
> > > > power to get something worthwhile here..."
> > >
> > > To start with, how big a box of water would it take to hold your
> > > molecule in its extended shape? What is your simulation rate for
> > > problems of this size?
> > >
> > > Bill
> > >
>
> _______________________________________________
> 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 Tue Sep 20 2011 - 23:00:02 PDT
