Hi,
You just need to pop a 'run' command after your first 'trajin' then
'clear trajin' so the first trajectory isn't used again, e.g.:
parm sys1.parm7 [sys1_parm]
reference sys1.rst7 parm [sys1_parm] [sys1_ref]
trajin sys1.nc parm [sys1_parm]
rmsd rmsd1 <mask> ref [sys1_ref] out rmsd.dat
run
clear trajin
parm sys2.parm7 [sys2_parm]
trajin sys2.nc parm [sys2_parm]
rmsd rmsd2 <mask> ref [sys1_ref] out rmsd.dat
run
This should work, let me know if not. Actions are cleared whenever
they are successfully used so you don't need to worry about the first
'rms' command being run twice.
You can also get the same effect by loading the trajectories as
COORDS/TRAJ data sets ('loadcrd'/'loadtraj') and using 'crdaction'.
Hope this helps,
-Dan
On Tue, May 27, 2014 at 8:43 AM, Brian Radak <radak004.umn.edu> wrote:
> I'd like to use cpptraj to calculate the RMSDs of several trajectories of
> different lengths and slightly different topologies (differences in
> protonation states and bound ions) with respect to the same reference
> structure.
>
> Here's some pseudo commands assuming two trajectories of "sys1" and "sys2".
> <mask> gives the exact same number of atoms for both systems.
>
> ==========
> parm sys1.parm7 [sys1_parm]
> reference sys1.rst7 parm [sys1_parm] [sys1_ref]
> trajin sys1.nc parm [sys1_parm]
>
> rmsd rmsd1 <mask> ref [sys1_ref] out rmsd.dat
>
> parm sys2.parm7 [sys2_parm]
> trajin sys2.nc parm [sys2_parm]
>
> rmsd rmsd2 <mask> ref [sys1_ref] out rmsd.dat
> ==========
>
> This does give me two data sets (rmsd1 and rmsd2) in rmsd.dat, as
> requested, but they include ALL of the frames loaded via trajin and both
> data sets are thus identical. Of course I'd like them to be different so
> that I can tell which rmsd values come from which trajectory/topology
> (although I suppose I could just do this by counting the frames, that
> sounds tedious and requires some kludgy scripting).
>
> Suggestions?
> Brian
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 27 2014 - 08:30:02 PDT
