Hello,When you minimize, you don't create a trajectory per se. That's why your file.nc 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" <stevesei.ku.edu> Date : 29/06/2020 18:22 (GMT+01:00) À : AMBER Mailing List <amber.ambermd.org> 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 <daniel.r.roe.gmail.com> Sent: Monday, June 29, 2020 10:11 AMTo: AMBER Mailing List <amber.ambermd.org>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 <stevesei.ku.edu> wrote:>> When I energy minimize in pmemd.MPI, I cannot read the trajectory output file "file.nc". 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> AMBER.ambermd.org> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cstevesei%40ku.edu%7C5e8cdfcb93474b5e5e6a08d81c3eb2df%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637290402897694316&sdata=I49nGyUARZr%2BYgaW3E74dYt6cbKk3jzrfSD1mQYjS0M%3D&reserved=0_______________________________________________AMBER mailing listAMBER.ambermd.orghttps://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cstevesei%40ku.edu%7C5e8cdfcb93474b5e5e6a08d81c3eb2df%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637290402897694316&sdata=I49nGyUARZr%2BYgaW3E74dYt6cbKk3jzrfSD1mQYjS0M%3D&reserved=0_______________________________________________AMBER mailing listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jun 29 2020 - 10:00:03 PDT
