Hi all,
Sander can now read the netcdf restart format as well as write.
Reading the format is currently controlled through the use of ntx.
ntx=8 reads coordinates only (analogous to ntx=1), and ntx=9 reads
coordinates and velocities. As with standard restart files the box
information is read in the ewald setup routines; the netcdf restart
format is automatically detected there.
The netcdf restart format could also be automatically detected in the
getcor() routine, but I figured it's better (at least initially) to
keep file behavior consistent. It can be easily changed so that ntx is
for example automatically chosen (8 or 9) if a netcdf restart is
detected as INPCRD and based on the value of irest.
Please experiment if you want and let me know if there are any
problems with the format.
-Dan
On Mon, Jan 10, 2011 at 1:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi All,
>
> I have implemented some experimental code in sander and cpptraj for
> reading and writing restart files in a netcdf format. Right now the
> restart includes coordinates and velocities (double precision), time,
> title, and (if performing REMD) replica temperature; they don't yet
> include any other info such as the state of the RN generator etc,
> although this should not be hard to add.
>
> To use the netcdf restart format in sander set ntxo = 2. Currently
> sander will only write the format - I'm working on the reading part
> now. Cpptraj will both read and write the format.
>
> -Dan
>
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Received on Tue Jan 11 2011 - 20:00:02 PST
