On Tue, Mar 23, 2010, Yang Li wrote:
> I'm trying to run a simulation of a 12mer DNA
> under 100 atm. In the beginning I tried to run it under constant pressure,
> here's my input file.
>
> imin = 0, ntb = 0,
Here you are requesting a non-periodic simulation, so the concept of pressure
is not relevant; you also set ntp=0, which turns off pressure coupling.
> I changed my input file to equilibrate the pressure.
You need to make sure you actually have a solvated, periodic prmtop file;
>
> The simulation ran for the entire weekend on a
> quadcore 3GB processor.
If you not sure whether your input is correct, don't run 100000 steps! Run
10 steps and set ntpr=1, then carefully examine your outputs to make sure
it is doing what you want.
....dac
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Received on Fri Mar 26 2010 - 08:00:05 PDT
