Dear Dr. Ross,
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.
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.
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 Mon Sep 19 2011 - 23:00:03 PDT
