AMBER Archive (2009)

Subject: Re: [AMBER] Am I doing the right thing

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Tue Jul 28 2009 - 22:44:59 CDT

See any system when solvated with a solvent, constitutes certain
number of molecules which needs to be considered for the simulation.
Obviously if that number is higher, it will demand more CPU hours to
leap through the energy surface to screen the energy minimum through
such a big confirmational space. CHCL3 thats why took less time, as it
is small, with less number of atoms. And i believe, the protein which
you are using is solvated with a pretty low number of CHCL3 as
compared to others.

On Wed, Jul 29, 2009 at 8:09 AM, Bill Ross<ross_at_cgl.ucsf.edu> wrote:
>> 2) While running the simulation with sander the molecule solvated with
>> CHCL3 is taking lesser that half the time taken by molecules solvated
>> in other solvents. Why is it so.
>
> What change took less than half the time?
>
> Bill
>
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-- 
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

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