On 4/29/20 7:49 AM, Max Winokan wrote:
My apologies for the missing images. Hopefully they are available along with 
the MDP in the following link: 

If anyone knows what could be going on, please let me know. Essentially the 
atom positions in the first NVT step are very different to the input topology, 
see my original email below.

Was there an intervening energy minimization step? The output of pdb2gmx looks fine, though providing the actual coordinate files and topologies themselves would be more useful for diagnosing the issue.

Note that if you are applying constraints, that operation is done before the first step so the coordinates can change. The distortion in the coordinates suggests and incorrect bonded topology.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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