[AMBER] Incorrect instructions in tutorial B1

From: Cavender, Chapin <Chapin_Cavender.URMC.Rochester.edu>
Date: Wed, 16 Oct 2019 23:23:27 +0000

Dear Amber developers,

A rotation student in my lab worked through tutorial B1 this week and found a couple of incorrect instructions.

1) In section 3.3.3, when loading the trajectory into VMD, the tutorial instructs the user to select "AMBER Coordinates" for the file type. This option does not work with the NETCDF format, and so "NETCDF" should be chosen instead.

2) In section 5.1.6 and 6.5, the input for the second run with explicit water uses "ntx = 7". This option is not read correctly by sander and causes the initial temperature to start from 0 K instead of 300 K. Using "ntx = 5" or running the job with pmemd fixes this behavior. The developers have indicated before (e.g.

http://archive.ambermd.org/201909/0305.html) that setting ntx to 5 and 7 is equivalent internally, but at least in this example with sander these options give different behavior.

Other users on the mailing list seem to have encountered both of these problems before: see http://archive.ambermd.org/201807/0007.html for the VMD option and http://archive.ambermd.org/201705/0036.html for the ntx option. Since this tutorial is the first impression of Amber for many users, you should consider fixing these instructions to be a priority.


Chapin Cavender

PhD student, Dave Mathews lab

Department of Biochemistry & Biophysics

University of Rochester Medical Center
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Received on Wed Oct 16 2019 - 16:30:01 PDT
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