My apologies, I was looking at the wrong mdin - the cutoff is 300 only
for the minimization, not the production run.
However, you should still run the included benchmarks and compare.
-Dan
On Mon, Mar 7, 2011 at 10:40 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You are running GB with an extremely large cutoff (300.0 Ang) so I
> think that 1.3 ns/day is not unreasonable for ~7600 atoms.
>
> Also note that your specific system setup (CPU, interconnect speed,
> compilers used etc) will impact your timing. You can run the
> benchmarks included with Amber and compare to existing benchmarks
> (http://ambermd.org/#benchmarks) to get an idea for how your system
> measures up.
>
> -Dan
>
> On Mon, Mar 7, 2011 at 10:04 AM, Rubben Torella
> <rubben.torella.gmail.com> wrote:
>> Dear Amber community,
>> I'm trying to perform MD simulation in implicit solvent using Generalized
>> Born approach on a protein-DNA complex.
>> I followed the tutorial described here (
>> http://www.uni-koeln.de/themen/chemie/software/amber7/tutorial/gb/gb_tutorial.html)<http://www.uni-koeln.de/themen/chemie/software/amber7/tutorial/gb/gb_tutorial.html>in
>> order to set-up the calculation.
>> We are talking about 7637 atoms in the complex.
>> I launched the calculation on 64 processors (10 ns), but the calculation
>> seems to me very slow (1.3 ns/day)
>> Is there something wrong in this approach or is it normal to have this
>> calculation speed?
>> I attached you the input of the MD calculation, in order to know if there
>> are mistakes or there is some flags that slow down the calculation.
>> Thank you for your help
>> Rubben
>>
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>>
>>
>
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Received on Mon Mar 07 2011 - 08:00:06 PST
