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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 11 2010 - 06:00:03 PDT
