[AMBER] Unable to view the box coordinates in VMD

From: Ramin Salimi <ramin.salimi01.utrgv.edu>
Date: Sun, 21 May 2017 17:55:32 +0000

Dear All
I have a .mdcrd trajectory file that I converted to .nc format using cpptraj.
When I load my trajectory file with .nc format, and choose Amber coordinate with periodic box as its type, it doesn't visualize the system in vmd giving the following message:
Using plugin crdbox for coordinates from file
Problem reading CRD file
Info) Finished with coordinate file
And when I choose the NetCDF(Amber, MMTK) option, it shows the solution but doesn't show the box.
Isn't it supposed to work for .nc formats?
The underlying reason to view the trajectory is that I have stretched my molecule and want to make sure that the molecule doesn't leave the box by the time it is fully stretched or during the extension, not rotated out of the box.
Is there any way other than the buffer size in leap to make sure that you have made an sufficiently elongated box so the stretched molecule doesn't exit the box?
One more question is that if I change the dimensions from the end of the inpcrd file, and then continue with minimization, heating, and equilibration, are the new dimensions going to be scaled back to the original ones by the end of equilibration?
My apologies if it has already been addressed.
Any help is appreciated.
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Received on Sun May 21 2017 - 11:00:02 PDT
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