Hi,
I'm not sure if you tried to send me any files or not. Are you still
having an issue with this? Another thing you might want to try is
simply visualizing the problematic frame in question to see if there
really is corruption.
-Dan
On Fri, Aug 27, 2021 at 6:54 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> First, what version of cpptraj are you using?
>
> Second, according to the output it seems like your 2nd frame might be corrupted (all coords are 0). Can you send me off list the topology and first 2 frames of the trajectory so I can try to reproduce the issue? Thanks.
>
> -Dan
>
> On Fri, Aug 27, 2021 at 2:32 AM Sadaf Rani <sadafrani6.gmail.com> wrote:
>>
>> 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
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Received on Tue Aug 31 2021 - 06:30:02 PDT
