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:
https://www.dropbox.com/sh/dnqz7c049f4tvw3/AAAGGZ8AF-ddQpBjD-QVf0OAa?dl=0
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
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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