Hi,
Do you mean you want the coordinate trajectory (i.e. the trajectory
following a single set of coordinates as it travels to different
replicas) as opposed to the replica trajectory? If so, there are two
cases to consider. If you ran T-REMD, the trajectories you get out are
actually coordinate trajectories (because temperature is what is
swapped between groups), so just read them in as normal. If you ran
H-REMD or M-REMD you can get coordinate trajectories via cpptraj by
using the corresponding replica logs to sort your ensemble into
coordinate trajectories, e.g.
ensemble rem.nc.000 remlog rem.log nstlim 500 ntwx 5000
here, nstlim and ntwx have the same meaning as they do in the &cntrl
namelist, steps between exchanges and steps between trajectory writes
respectively.
Hope this helps,
-Dan
On Mon, Jul 24, 2017 at 3:59 PM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
> Hello,
>
> I have a curiosity: I have a nc trajectory obtained from REMD, so the
> frames are actually not-consecutive snapshots. Is there a tool to align the
> protein from frame to frame?
>
> I'm performing cluster analysis on it, and would like to be sure that this
> issue is not a problem in calculating RMS and average structures. Right
> now, average structures are completely unrealistic.
>
> Suggestions?
>
> Elisa
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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 Tue Jul 25 2017 - 06:00:06 PDT
