Re: [AMBER] pmemd.MPI and minization trajectories

From: Seibold, Steve Allan <>
Date: Mon, 29 Jun 2020 16:22:48 +0000

Hi Dan
Thanks for the response. Yes, I have ntwx set at 250 using pmemd.MPI. I also have tried with and without "ioutfm = 1". In neither case could cpptraj read the trajectories.
 When I use sander.MPI (without "ioutfm" or with "ioutfm=1"), cpptraj IS able to read the trajectory files..strange.


-----Original Message-----
From: Daniel Roe <>
Sent: Monday, June 29, 2020 10:11 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] pmemd.MPI and minization trajectories


Do you have ntwx > 0 in your MDIN file?


On Mon, Jun 29, 2020 at 11:09 AM 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?
> Thanks, Steve
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