yes that was the error a straight line - it did not make any sense. sure it
is constant and I have check the files and I am doing the reimaging but I
though the amber coordinates with PBC in VMD would actually do this for one
but no yet
On Wed, Aug 11, 2010 at 2:30 PM, Andrew Purkiss-Trew <
a.purkiss.mail.cryst.bbk.ac.uk> wrote:
> On Wed, 2010-08-11 at 07:41 -0400, case wrote:
> > 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.
> >
>
> I believe that this increasing volume is due to the data being
> misplotted. As you say the pressure is set to zero in the .out file, but
> the volume isn't even printed. This means that the processing script
> (process_mdout.perl), which converts the mdout file into the summary
> files, just gives the time values in the summary.VOLUME file with the
> corresponding volume data left blank.
>
> Some plotting programs this as a straight line (time v time). You need
> to look at the dimensions in the restart file, to check the volume
> correctly.
>
>
>
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Received on Wed Aug 11 2010 - 06:00:04 PDT
