Hi,
Sounds like you want to use 'ensemble' mode with 'nosort' if
everything is already sorted by temperature. Something like:
parm HYN.strip.parm7
ensemble remdfull.temp.strip.nc.1 nosort
strip .Cl-
...
See the manual for full details. FYI in MPI versions of cpptraj the
'ensemble' command can be used with 1 or more threads per ensemble
member to speed things up.
-Dan
On Mon, Dec 18, 2017 at 5:14 AM, Andreas Tosstorff
<andreas.tosstorff.cup.uni-muenchen.de> wrote:
> Hi all,
>
> I am trying to use cpptraj on a set of T-REMD trajectories. I have a
> traectory for each temperature and now I want to calculate a number of
> properties for each temperature, such as e.g. average surface area of
> the protein.
>
> My cpptraj input looks like this:
>
> parm HYN.strip.parm7
> trajin remdfull.temp.strip.nc.1
> trajin remdfull.temp.strip.nc.2
> trajin remdfull.temp.strip.nc.3
> ...
> trajin remdfull.temp.strip.nc.63
> strip .Cl-
> autoimage
> surf HYN_surf :4-284 out HYN_surf.dat
> avg HYN_surf out HYN_surf_avg.dat
>
> run
> quit
>
> However this results in just one average surface over all temperatrures.
> What's the easiest way to treat each trajectory seperately?
>
> Thanks a lot for your help!
>
> Andreas
>
>
> --
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> Department Pharmazie
> LMU München
> Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Dec 18 2017 - 11:00:02 PST
