Re: [AMBER] pupil and amber

From: Ben Roberts <>
Date: Wed, 23 Dec 2009 13:59:04 +1100

Hi Davide,

I think you may have stumbled across an incomplete patch. -jxms, -jxmx etc
are present in Amber 11 but not yet Amber 10. They exist to provide better
user control over maximum memory allocation to JVMs launched from within

I think the best solution is for my PUPIL colleagues and I to prepare a
further patch for Amber 10. I can't say when that will be done; I'm out of
the office at the moment and return to work in early January. I'm happy to
notify you of the new patch if you would find that helpful. If a new patch
isn't possible, I'll try to come up with another way forward for you.

Best regards,

Ben Roberts

----- Original Message -----
From: "davide branduardi" <>
To: <>
Sent: Wednesday, December 23, 2009 7:29 AM
Subject: [AMBER] pupil and amber

> Dear All,
> I'm trying to use AMBER10 together with PUPIL to do a qmmm calculation.
> The setup of amber10 (bugfixed with the latest patch) with make
> sander.PUPIL
> works fine and the setup of pupil runs fine as well.
> Unfortunately when I run the tests (ala3 with g03)
> I got some problems specifically connected with the amber code
> The line that pupil call is
> ./sanderLinux -O -i mdin -p ala3.parm7 -c ala3.inpcrd -ORBInitialPort 3001
> -ORBInitialHost baldios -OptPrint 5 -jxms 64 -jxmx 4096 -jxss 16
> (where sanderLinux is a link to sander.PUPIL )
> but sander ends up with an error which is
> mdfil: Error unknown flag: -jxms
> usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
> rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo
> -radii radii -y inptraj]
> Consult the manual for additional options.
> In fact mdfil.f (After being patched with pupil) routine does contain
> ORBInitialPort -ORBInitialHost -OptPrint options but not -jxms
> -jxmx -jxss.
> I suspect that these are connected with CORBA and this make me think that
> probably my java installation or the runtime
> environment is not properly set.
> Anyone can help me?
> Best regards
> Davide

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Received on Tue Dec 22 2009 - 19:00:03 PST
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