> 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
> >
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Received on Tue Sep 20 2011 - 10:30:02 PDT
