Dear Amber users
I ran a simulation for 100ns, during rmsd calculation I am getting this
error message from frame 1 to frame 2070 are corrupt as mentioned below:-
Warning: Frame 2070 imaging failed, box lengths are zero.
I tried to do "check" in cpptraj and got the following error message:-
ACTION SETUP FOR PARM 'complex_wild.prmtop' (1 actions):
0: [check]
Total Grid memory: 741.376 MB
TIME: Pair List Setup: 1.4803 s
Grid dimensions: 80 80 80 (512000 total).
Using pair list.
Mask [*] corresponds to 130368 atoms.
Checking 130462 bonds.
Imaging on.
----- prod_md_100ns.nc (1-50000, 1) -----
0% Warning: Frame 2 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Unit cell size has changed so much that grid must be recalculated.
Warning: Old sizes= {80, 80, 80} New sizes= {1, 1, 1}
Warning: X cell offset reset to 1
Warning: Y cell offset reset to 1
Warning: Z cell offset reset to 1
Total Grid memory: 3.129 MB
Killed
Could you please share your expert opinion on why is it happening to unit
call and how should I fix this?
Regards
Sadaf
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 27 2021 - 00:00:02 PDT
