Good afternoon: I am running simulations using a truncated octahedron water
box. I do not wrap the water during the simulation ( iwrap=0 ), however I
do rewrap the restart file using cpptraj and the following input script:
############
parm prmtop/mut.prmtop
trajin data/md2.rst7
autoimage origin
trajout data/md2-recenter.rst7
############
When looking at the input file, I notice that the cumulative time is
incorrect after I rewrap (i.e. the begin time read by Amber is 1 ps),
despite the fact that I set the flags to read in coordinates and velocities
for restarting. I wanted to confirm that the rewrapping is not affecting
the velocities for restart. If I do not rewrap, then the begin time is read
normally. I checked and the file sized of the unwrapped and rewrapped
restart files are the same, so all of the information should be there.
Thanks in advance!
Geoffrey
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Received on Mon Sep 08 2014 - 09:30:02 PDT
