Re: [AMBER] Error with NVT and NPT Simulations

From: Daniel Roe <>
Date: Mon, 9 Sep 2013 15:42:24 -0600


> lines, respectively. The graduate student I work under informed me there
> should be twice as many lines in the NVT.restrt file; however, it is three

This is not strictly true. The Amber ASCII restart format is:

Title line
Natom [time] [temp0]
<Natom * 3 Coordinates>
[<Natom * 3 Velocities>]
[Box Info]

In your initial restart (presumably from a minimization) there is no
velocity information, whereas in your MD restart you do have velocity
information. Therefore the number of lines in the MD restart (M)
compared to the number of lines in the Min restart (N) should be:

M = ((N - 3) * 2) + 3
M = 2N - 3
(if you had no box info it would be M = 2N - 2)

So the number of lines in your second restart appears fine (this of
course doesnt preclude their being some other kind of problem with the
restart). You could do some basic checking of the restart via the
'check' command in cpptraj.

Your best bet when troubleshooting an error like this is to simplify
the run as much as you can. So try running only a few steps (10-100)
using the serial version of the code, printing out information every
step. Sometimes error messages are harder to find when running
multiple threads.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Sep 09 2013 - 15:00:02 PDT
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