Re: [AMBER] simulation under pressure

From: case <>
Date: Fri, 26 Mar 2010 10:54:10 -0400

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.


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Received on Fri Mar 26 2010 - 08:00:05 PDT
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