Hi,
I presume you are referring to the keywords for the 'rmsd' action. You
can specify an external reference structure for an rms command in
three different ways:
refindex <#>: Use reference structure read in by a previous "reference
<filename>" command, where <#> is the order the reference was read in.
ref <filename>: Use reference structure read in by a previous
"reference <filename>" command.
reference: Short for "refindex 0" (first reference structure read in),
included for backwards compatibility with ptraj.
For example, given the script:
trajin mdcrd
reference ref1.rst7
reference ref2.rst7
rmsd reference :1-10 out r1.dat
rmsd refindex 1 :1-10 out r2.dat
rmsd ref ref2.rst7 :1-10 out r2.dat
The first rms command will use ref1.rst7 as a reference, and the last
two rms commands will use ref2.rst7 as an index. See the manual for
more details. Let me know if you still have questions.
-Dan
On Mon, Jun 13, 2011 at 6:39 AM, Xiao Chen <chen.xiao.po.gmail.com> wrote:
> Hi All,
>
> Can you clearly elucidate the difference between the keywords "ref" and
> "reference" in cpptraj.
>
> Thanks!
>
> Po
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Received on Mon Jun 13 2011 - 08:00:04 PDT
