Re: [AMBER] MD run saving only 250 frames

From: Jeyaram R A <>
Date: Wed, 17 Jan 2018 07:14:29 +0000

             The Amber trajectory file is depending upon the nstlim and ntwx. In your case nstlim = 25,000,000 and ntwx = 10,000 so definitely you will get 2500 frames. But you mentioned you got only 250 frames, i can't believe this. Meantime your ntpr = 1000, so will get 25000 mdout files. How many out files you got from the simulation?, My suggestion is if you are reducing the ntpr = 500 and ntwx = 500 you will get 50,000 out files and 50,000 frames.

with regards,
R. A. Jeyaram
From: Paul Meister <>
Sent: Wednesday, January 17, 2018 1:28 AM
To: AMBER Mailing List
Subject: [AMBER] MD run saving only 250 frames

Hello AMBER users,

I am having an issue with trying to run a 50 ns simulation on an enzyme. We
have recently started using AMBER16 from AMBER14 and have copied over the
production .in files we used for that version. I have attached the
file and md.bash file for reference. I have tried running the input command
separately as well as with the bash script and also as .crd output format.
The input command was:

pmemd.cuda -O -i -o md.out -p -c md.incrd -r md.rst -x
-ref md.firstcrd -inf md.mdinfo

After I try to load the nc file with VMD or use cpptraj, there are always
only 250 frames in the file. Is there something I am missing in the
.in file preventing me from saving more than 250 frames?

Thank you for your suggestions,


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Received on Tue Jan 16 2018 - 23:30:02 PST
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