Ok..great, thanks for the response. I think I will try the ntwx = 5 or so....
Steve
-----Original Message-----
From: David A Case <david.case.rutgers.edu>
Sent: Monday, June 29, 2020 1:19 PM
To: AMBER Mailing List <amber.ambermd.org>
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 "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?
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.).
....dac
_______________________________________________
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%7C628426aaf4c74f2d4dbc08d81c58e03f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637290515325714782&sdata=VwyVXQ3eQDnXJYID2b1Bf%2BimVfhMHizGXbShkqQRhuc%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 29 2020 - 12:00:04 PDT
