From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Sep 08 2016 - 01:41:21 CDT
What kind of REMD did you perform? Just normal parallel tempering? If so, you should get all the frames in the sorted dcds for which you also have the corresponding history entry. Also, how did you call sortreplicas?
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Horia Jalily Hasani
Gesendet: Donnerstag, 8. September 2016 02:11
An: <namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu>
Betreff: namd-l: REMD and sortreplicas program
I have been performing REMD and I wonder if someone could give me a hint in the analysis part. When it comes to using the sortreplicas for sorting the dcd files and history files based on temperature, the program seems to take "only frames with the biasing potential V (d, i)" (quoted from the One-dimensional REUS tutorial).
For example, if I give it trajectories each of which have 2000 frames, I end up getting only 50 frames in the sorted dcd files. But I am interested in having all the 2000 frames sorted based on temperature without considering the potential at that point.
I would appreciate if anyone could give me a hint related to the sortreplicas program and if there is an alternative way of sorting the outputs based on temperature.
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