[gmx-users] Atom positions change between topology generation and NVT equilibration

[Justin Lemkul]

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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