Re: [AMBER] pmemd.MPI and minization trajectories

From: Seibold, Steve Allan <>
Date: Mon, 29 Jun 2020 18:38:51 +0000

Ok..great, thanks for the response. I think I will try the ntwx = 5 or so....


-----Original Message-----
From: David A Case <>
Sent: Monday, June 29, 2020 1:19 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] pmemd.MPI and minization trajectories

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 want.).


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