Re: [AMBER] pmemd.MPI and minization trajectories

From: David A Case <>
Date: Mon, 29 Jun 2020 14:18:38 -0400

On Mon, Jun 29, 2020, Seibold, Steve Allan wrote:

>When I energy minimize in pmemd.MPI, I cannot read the trajectory output
>file "". The error in cpptraj is "Netcdf file is empty". If I run
>imin =0, and do conventional MD, there is no problem. The cpptraj package
>reads the trajectories just fine. Am I missing a flag in the input file
>that is not allowing me to visualize the minimization trajectories?

Gerald is correct: you can't get a traditional "trajectory" file from
minimization. But (untested!) I think you can set ntwr=-5 which will
give a restart file every 5 steps (change "5" to whatever frequency you


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Received on Mon Jun 29 2020 - 11:30:04 PDT
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