[AMBER] Unit cell size has changed in trajcetory

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Fri, 27 Aug 2021 11:32:32 +0500

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

Could you please share your expert opinion on why is it happening to unit
call and how should I fix this?
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Received on Fri Aug 27 2021 - 00:00:02 PDT
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