On Tue, Jun 10, 2008, xiaonan zhang wrote:
>
> xleap did not report error. As to your first suggestion, could you give
> me some detailed about it or where can I find the relevant commands in the
> manual. I really have no concept on the unit cell.
Look for the "image" command in ptraj.
>
> In addition, there is another question about temperature.
> As the input file define the target temperature as 30K,
> but mdout file showed much higher temperature,
>
> NSTEP = 100 TIME(PS) = 0.100 TEMP(K) = 74.26 PRESS =
Look at how the temperature varies as a function of time. It takes a while
to "settle down" to a given temperature.
It sounds like you need to work through some of the tutorials (if you haven't
already done so). The basic tutorials address many of the questions you are
having, and you can see what outputs "should" look like for a standard
simulation.
...dac
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Received on Sun Jun 15 2008 - 06:07:17 PDT
