AMBER Archive (2004)

Subject: Re: AMBER: PMEMD Problems...

From: Jon Gray (
Date: Mon Apr 05 2004 - 22:56:47 CDT


Sorry, that -C was a typo and was meant to be a lowercase -c

To give you more detail, the system I am attempting to run PMEMD on is a
2GHz P4 (single processor). I compiled with ifc 7.1.008 on a redhat 7.3
distribution. Have you seen a successful run on that version of redhat or
would you recommend me trying redhat 9? I have also attempted an install
on a Suse 9.0 system but could not even get amber7 to compile, so did not
attempt to do PMEMD.

Also, is this 'Terminated Abnormally' message normal for improper
parameters, or could this mean the compiled binary is bad? I would like to
figure out whether this is an issue with the system and compiling of PMEMD
(my area) or an issue with the usage and syntax with the PMEMD program
(someone elses).

Thanks again for your help.

-Jon Gray

--On Monday, April 05, 2004 5:13 PM -0400 Robert Duke <>

> 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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