Hi,
As per your suggestion, I tried to do small simulation as follows:
1) heating at ntb=1; the last line of restart file after the heating is:
85.0300000 85.0300000 85.0300000 109.4712190 109.4712190 109.4712190
which is exactly identical to what I got from tleap.
2) equilibration at ntb=2; the last line of restart file is:
85.1454891 85.1454891 85.1454891 109.4712190 109.4712190 109.4712190
As you can see, the values are not identical to what has been previously
reported.
Now your suggestion??
Thanks,
Hirdesh
**
On Fri, Sep 30, 2016 at 1:22 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Fri, Sep 30, 2016, Hirdesh Kumar wrote:
> >
> > .Dan: I checked the prmtop file specification (
> > http://ambermd.org/formats.html) for BOX_DIMENSIONS and it says:
> >
> > OLDBETA : periodic box, angle between the XY and YZ planes in
> > degrees.
> >
> > *This is now redundant, as it is present in the
> > inpcrd files. It is ignored here.*
> >
> > Does it mean that even if I dont change these values in prmtop file then
> > also it is fine because I have modified the last line of restart file
> from :
> > 90.0 to 109.4712190?
>
> Yes.
>
> >
> > .Dac: My restart file is netcdf formatted so I can not visualize it using
> > vi editor.
>
> Run a (short) simulation with ntxo=1...that will create a restart file with
> the old format, where you can check the last line. (You can also use
> cpptraj
> to convert the netcdf restart to ascii restart, and look at that.)
>
> >
> > The last line of my original restart file (copied from inpcrd file which
> I
> > generated using tleap):
> > * 85.0300000 85.0300000 85.0300000 109.4712190 109.4712190 109.4712190*
>
> Above is correct.
>
> > The last line of the inpcrd file which I generated after 26ns:
> > * 85.058 85.058 85.058*
>
> Above is incorrect. If you generated this by tleap, you need to edit it to
> add the angles. As stated above, it *may* be the case that setting ifbox
> to 2
> in the prmtop file may accomplish the same objective, but I'm not sure
> about
> that. That is why you need to run a short simulation with the new system
> to
> check how the boxes are being handled.
>
> ....dac
>
>
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Received on Fri Sep 30 2016 - 05:30:04 PDT
