Hi All,
This is minor but I figured I would get opinions anyway.
According to the current manual:
"The time at the start (psec) this is for your own reference and is
not critical. Start time is taken from the coordinate input file if
IREST=1. Default 0.0."
My interpretation of this is that when irest=1 the time is whatever is
in the restart file, otherwise it is whatever is specified by 't', or
zero if not specified. However in both sander and pmemd this is
currently not the case. The initial time is always taken from the
restart file; even when irest=0 and 't' is specified, the value of 't'
is overwritten by the one from the restart.
I'm not sure how long the behavior has been this way but it's been
long enough that fixing this behavior changes the output of a number
of tests. My personal opinion is that the behavior should be corrected
since it can be misleading to have an irest=0 run always continue from
the previous time (perhaps later on giving the illusion that the run
was continuous).
Thoughts?
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue May 26 2015 - 09:00:02 PDT
