AMBER Archive (2004)

Subject: Re: AMBER: PMEMD and nmropt=1

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Feb 05 2004 - 06:39:58 CST

Aldo -
I am pretty much the "pmemd guy". If you are having a problem with pmemd,
and the same input runs okay in sander 7, please send all input and output
to me and I will debug the problem (also let me know what platform and what
MACHINE file you used). With pmemd, nmropt=2 is not supported, but all the
nmropt=1 options are supposed to work. However, getting test coverage of
everything done under nmropt=1 is a bear so there is the possibility of a
problem (I did not do much at all to change the nmr code, though). Also let
me know your pmemd version.
Regards - Bob Duke
----- Original Message -----
From: "aldo jongejan" <jongejan_at_few.vu.nl>
To: <amber_at_scripps.edu>
Sent: Thursday, February 05, 2004 6:52 AM
Subject: AMBER: PMEMD and nmropt=1

> Dear all,
>
> I am trying to run similar jobs as I have ran with AMBER 7 in PMEMD,
> but am not able to get the jobs running. It seems that the nmropt=1
> option is causing the trouble, as jobs without these restraints ran
> smoothly.
> I have read the mails of Kristina Furst and Robert Duke, but my runs
> don't even get that far...they stop producing output after echoing the
> input-deck and the title of the run. The job hangs after this..
>
> Maybe something goes wrong in the calls to MPI, but I wondered
> if somebody could help me, before diving into the source code :-)
>
> greetings,
>
> aldo
>
> --
> ###########################################
>
> Aldo Jongejan
> Molecular Modeling Group
> Dept. of Pharmacochemistry
> Free University of Amsterdam
> De Boelelaan 1083
> 1081 HV Amsterdam
> The Netherlands
>
> e-mail: jongejan_at_chem.vu.nl
> tlf: +31 (0)20 4447612
> fax: +31 (0)20 4447610
>
> ###########################################
>
>
>
>
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