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 - 04:30:02 PDT
