Thank you fro you help, I have found a mistake in the script to run the MD.
I have fix it!
2016-10-24 13:58 GMT+02:00 David A Case <david.case.rutgers.edu>:
> On Mon, Oct 24, 2016, Stefania Mirabella wrote:
>
>> I am running MDs with Amber of ligand-protein complexes of 20 ns. When
>> I used a small ligand (MW about 300 Da) the dynamic was long 3-4 days,
>> but when I changed to a ligand three times bigger (around 900 Da) the
>> time is dramatically increased to 330 days!
>
> Something seems quite wrong. Amber MD programs print out timings details at
> the end of each run...look at those to see if you can see what is different
> between the two runs.
>
> MD times are generally, and roughly, linear in the number of atoms being
> simulated. Since your protein is probably(?) much bigger than you ligand, the
> two simulations should take about the same amount of time.
>
> As you can appreciate, no one will be able to provide more specific
> information based on the single sentence description provided above.
>
> ....dac
>
>
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Received on Mon Oct 24 2016 - 06:00:04 PDT
