Hi Hannes,
This is a general framework developed with the aim to interface
different programs for multi-scale calculations. More specifically, it
supports QM/MM MD simulations where the user might choose among any of
the different MD engines and QM engines, which are connected to PUPIL as
external programs through a tiny specific interface. One of the main
advantages here is that the user can use most of the functionalities
that may have those external programs interfaced without the necessity
to be reimplemented again on independent interfaces. In fact, this
simulation interface concentrates all the common code involved in the
coupling terms of the QM/MM approach. That allows an easy implementation
of new external MD and QM programs to be interfaced.
This software is addressed to those users that might want to
perform QM/MM MD simulations using the already connected programs or to
those developers that might be interested in other external programs
that are not yet interconnected and they want to use PUPIL to build the
interface without much additional programming.
Regards,
Joan
El 09/12/2014 8:42, hannes.loeffler.stfc.ac.uk escribió:
> Hi,
>
> this looks certainly interesting but from this email and the front page at sourceforge it is a bit unclear what exactly this code does. You say it is multi-scaling. In what sense? I spot there two MD codes and a few semiempirical/QM/etc codes. So I suspect you can do QM/MM type of calculations. What would be the advantage of your solution over existing ones? Are you primarily addressing developers?
>
> Many thanks,
> Hannes.
>
> ________________________________________
> From: Joan Torras [joan.torras.upc.edu]
> Sent: 08 December 2014 23:36
> To: amber.ambermd.org
> Subject: [AMBER] Software announcement: Release of PUPIL 3.0
>
> We are pleased to announce the release of PUPIL 3.0.
>
> PUPIL (Program for User Package Interface and Linking), is a software
> environment that allows users and developers to link quickly and
> efficiently together multiple pieces of software in a fully automated
> multi-scale simulation.
>
> * Graphic User Interface to build the main simulation input file.
> * Simulation Manager to lead the multi-scale simulation between different external programs.
> * Interface with Amber v10, 11, 12, and 14
> * Interface with DeMon2k 4.2.4
> * Interface with DL_CLASS_1.9 (DLPOLY)
> * Interface with NWChem v6.1.1 and v6.5
> * Interface with Gaussian 03 and 09
> * Interface with Siesta v3.2 (Start/Stop and CycleQM behaviors)
> * Interface with MNDO97 (Start/Stop QM role behaviors)
> * stubMD. Stub program for interface sample and testing playing a Molecular Dynamics Calculation Unit role.
> * stubQM. Stub program for interface sample and testing, playing a Cycle Quantum Mechanics Calculation Unit role.
> * stubDI. Stub program for interface sample and testing,playing an external Domain Identifier Calculation Unit role.
>
> New Features:
>
> * DL_CLASS program incorporates the electrostatic embedding scheme through the PUPIL interface.
> * PUPIL package has been updated to be compatible with Java 1.7 and 1.8.
> * A new interface with NWChem 6.3 and 6.5.
> * Some bottle-neck on the neighborhood rules has been fixed through the parallelization on the PUPIL core.
> * An initial alpha version using Long-range electrostatics on the QM region has been implemented
> * More accurate numerical checks are incorporated when the output files of tests cases are compared.
>
> For full details of PUPIL's features and capabilities, visit our web page:
>
> http://pupil.sourceforge.net/
>
>
> The PUPIL Team.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Joan Torras-Costa
Department of Chemical Engineering
EEI, Universitat Politècnica de Catalunya (UPC)
Av. Pla de Massa, 8
08700 - Igualada
SPAIN
Telf.: +34 93 803 5300
Fax : +34 93 803 1589
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 09 2014 - 01:00:03 PST
