Thanks, that worked. A nice option might be to have cpptraj detect NaN's
and stop reading. :-)
The interesting result is that I can't just scale selected atoms'
velocities up to impart user 'taps' to my molecule, since the
reinforcement of modes seems to be causing blowup, rather than
collisions. Adding an orthogonal velocity component may work better.
Bill
On 8/25/16 1:47 PM, Hai Nguyen wrote:
> may be you can use cpptraj to compute the center of mass (or anything else)
> of your trajectory, plot the output to see the messed up frames?
>
> If you know specific frame, you can specify *trajin my.mdcd 1
> your_given_frame*?
>
> Hopefully I understand your question correctly.
>
> Hai
>
> On Thu, Aug 25, 2016 at 4:26 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> I have a netcdf mdcrd file in which the energies went south due to my
>> user interactivity feature.
>>
>> When I try to load the mdcrd in VMD, nothing happens except this
>> informative console message:
>>
>> Info) Using plugin crd for coordinates from file
>> amber14/proj/cat_md62.crd
>> Problem reading CRD file
>> Info) Finished with coordinate file amber14/proj/cat_md62.crd.
>>
>> I'd like to watch how the blowup occurred - is there some way to repair
>> the netcdf up to that point, so I can watch what happens?
>>
>> Thanks,
>>
>> Bill
>>
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>>
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Received on Thu Aug 25 2016 - 16:00:03 PDT
