Re: [AMBER] pmemd.MPI and minization trajectories

From: Gerald Monard <>
Date: Mon, 29 Jun 2020 18:53:53 +0200

Hello,When you minimize, you don't create a trajectory per se. That's why your is empty. As far as i know, i don't think that there is a way within Amber (nor sander nor pmemd) to save the intermediate geometries occuring during a minimization.Best,Gerald.Envoyé depuis mon smartphone.
-------- Message d'origine --------De : "Seibold, Steve Allan" <> Date : 29/06/2020 18:22 (GMT+01:00) À : AMBER Mailing List <> Objet : Re: [AMBER] pmemd.MPI and minization trajectories Hi DanThanks 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.Steve-----Original Message-----From: Daniel Roe <> Sent: Monday, June 29, 2020 10:11 AMTo: AMBER Mailing List <>Subject: Re: [AMBER] pmemd.MPI and minization trajectoriesHi,Do you have ntwx > 0 in your MDIN file?-DanOn 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> _______________________________________________> AMBER mailing list>>;;sdata=I49nGyUARZr%2BYgaW3E74dYt6cbKk3jzrfSD1mQYjS0M%3D&amp;reserved=0_______________________________________________AMBER mailing listAMBER.ambermd.org;;sdata=I49nGyUARZr%2BYgaW3E74dYt6cbKk3jzrfSD1mQYjS0M%3D&amp;reserved=0_______________________________________________AMBER mailing listAMBER.ambermd.org
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Received on Mon Jun 29 2020 - 10:00:03 PDT
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