Re: AMBER: PMEMD Problems...

From: Robert Duke <>
Date: Mon, 5 Apr 2004 17:13:24 -0400

Jonathan -
The one thing I see right off is the use of -C to specify input coordinates
instead of -c. The input arguments are case sensitive. If you enter
"pmemd -help" you will get a list of allowed input parameters, but you will
have to read the manual to figure it all out. The basic procedure is to
start with a knowledge of sander, look at the pmemd manual section for the
delta's in behaviour, and have at it. PMEMD should take close to the same
input. If you are dealing with pmemd 3.0-3.1, there is a help facility that
is invoked with "pmemd -help", analogous to the help facility that was in
sander 6. This has been dropped in both pmemd 8 and sander 8; the sander
guys I presume dropped it due to the headaches involved in keeping it up to
date; I dropped it in 8 because they did, and also it was a pain to keep up
to date in pmemd also. You give no info about your systems other than the
compiler, so I can't be much more help. If you run under mpi, you of course
have to invoke with an mpi-specific command rather than just the executable
name, and there are definite touchy issues involved in getting mpi stuff
built under linux. There has been a fairly active discussion on the amber
reflector as of late dealing with the problems encountered with the latest
releases of linux and the intel fortran compiler. I have recently gotten
everything running with the latest redhat, fully updated (3.x rhel), redhat
9 (also fully updated), ifc 7.1.038 (7.1.040 is broken, ifort 8 seems to be
perpetually hopeless), and +/- mpich I have gotten it all running
on 3.2 GHz dual pentiums, but gave up on a dual opteron (2.2 GHz) that was
apparently overheating. You are nowhere near heating problems yet, though
Regards - Bob Duke

----- Original Message -----
From: "Jon Gray" <>
To: <>
Sent: Monday, April 05, 2004 4:38 PM
Subject: AMBER: PMEMD Problems...

> Hello everyone,
> I have been trying to install PMEMD to be used with our existing amber7
> installation for a couple weeks now. At first I was having issues with
> version 8 of the intel fortran compiler, but after switching to an older
> version of 7 it seemed to compile smoothly.
> Although it is compiled now, whenever I execute the pmemd binary file I
> just get:
> FORTRAN STOP PMEMD Terminated Abnormally!
> There is no output of an error file whatsoever. This happens when I just
> execute the command by itself (although then I get an mdout error along
> with the Terminated Abnormally message) or when
> I try running something that runs fine under sander. Here is line I am
> attempting to execute:
> pmemd -O -i sander_V_PMEMD.inp -o a_m.out -p \
> -C a_m.V169ps.rst -r a_m.rst -ref a_m.V169ps.rst -x a_m.trj
> Forgive me if I misused some terminology, or this is an obvious problem, I
> am not actually in this field but rather just a tech person who has been
> assigned this problem :)
> Thank you in advance.
> -Jonathan Gray (Carnegie Mellon University Chemistry Dept)
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Received on Mon Apr 05 2004 - 22:53:01 PDT
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