Extra frame at start of each trajectory

From: Ethan Croitoru (ecroitoru1_at_gmail.com)
Date: Wed Aug 05 2020 - 14:23:47 CDT


I am running a Martini coarse-grained system with NAMD, built following the
tutorial (
http://www.ks.uiuc.edu/Training/Tutorials/martini/rbcg-tutorial.pdf). My
system is a protein in a membrane, so I used the conf files for the extra
example M2-channel to run minimization and equilibration. The tutorial
splits equilibration into 5 jobs, and for the first 2 jobs everything is
normal, but at the third job there is an extra frame at the beginning of
the trajectory that does not have periodic images (as I have set pbc). The
only difference in the 2nd and 3rd job's conf file is the
constraint scaling and input and output names, so I don't understand how
this issue started to occur, but every job after the 3rd equilibration job
has included that extra frame. The 2nd and 3rd equilibration job both run
for the same time, but the 3rd trajectory has the extra frame in addition
to the simulation with regular pbc, as in the 3rd trajectory has an added
frame, rather than a frame with bad pbc. Can anyone explain why this is
happening or how to stop it?


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