On Wed, Aug 11, 2010, Jorgen Simonsen wrote:
>
> I am equilibrating my system raising the temperature from 0 to 300K - I want
> to start by also equilibrating the pressure doing my simulation in NVT
> enzemble so I set my variables using constraits on my protein backbone (10
> kcal/mol)
>
> ntb = 1,
> cut = 12.0,
>
> when I look at my results in VMD the only thing that has really changed is
> the box which is no longer square but a strange form.
This sounds like an imaging issue--be sure to re-image using ptraj before
looking at the atomic coordinates in VMD.
> Furthermore if I plot
> volume and pressure from the output file the volume is increasing and the
> pressure is at 0
This sounds like a serious problem, since the volume should be constant.
The pressure is reported as zero since it is not computed in NVT
calculations--the zero is just a placeholder. Please double-check that you
are really seeing the volume increase--manually inspect the mdout file, and
look at the last line of the restart file, where the box size is placed.
....dac
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Received on Wed Aug 11 2010 - 05:00:03 PDT
