Hello Lucio,
Thanks for making us aware of this interesting way of using AMBER. I visited the website your refer to below and have a couple of questions.
Is the web portal ONLY for use of the computing facilities in Europe associated with e-NMR?
Can the web portal be exported to another location to allow the use of AMBER via such a web gui at another university? That is, can the web program be provided for use elsewhere to run AMBER, for example, at my installation?
I am in the US. The registration page at the SB Grid states that all jobs must be between 10 min and 10 hours. MD can run for weeks to months, depending on the system under study. This would imply that it would be best if a research group used its own hardware for such jobs. Thus it would be interesting to obtain the WEB GUI for AMBER, but not necessarily to run the jobs in Europe. Is that possible?
Thanks, Sergio
Sergio Aragon
Professor of Chemistry
San Francisco State University
-----Original Message-----
From: Lucio Ferella [mailto:ferella.cerm.unifi.it]
Sent: Monday, September 20, 2010 5:11 AM
To: amber.ambermd.org
Subject: [AMBER] GRID-enabled web portal for the use of the AMBER
Dear All,
I am informing you that we have recently developed a GRID-enabled web
portal for the use of the AMBER molecular dynamics package, which was
developed by CERM researchers within a EC FP7 funded project (Contract
no. 213010 – e-NMR).
This portal allows an easy access - with a common web browser - to the
main functionalities of AMBER, and, in particular, provides a means for
a user-friendly set up of common and advanced AMBER parameters.
The portal allows researchers to:
- perform a completely automated refinement of protein structures, based
on molecular dynamics in explicit solvent;
- have a fast throughput of their results, thanks to the totally
transparent grid computing infrastructure;
- access all their data easily via the web while keeping full security;
- navigate across, browse, visualize and download data for all their
jobs thanks to the hierarchical organization in project directories
provided by the portal;
- user-friendly interact with the jobs highlighting their currently
status (scheduled, running, canceled, terminated) as well as retrieve
results.
I really hope you (and your students and post-docs) will try our
GRID-enabled web portal for the use of the AMBER visiting either of one
of these two links:
-
http://py-enmr.cerm.unifi.it/
OR
-
http://www.enmr.eu/webportal/ (and clicking on <AMBER> menu item)
Sincerely,
Lucio Ferella
-------------------------------------------------------------------------
Lucio Ferella
CIRMMP - Consorzio Interuniversitario Risonanze
Magnetiche di Metalloproteine Paramagnetiche
CERM - Magnetic Resonance Center
Via Sacconi, 6 - 50019 Sesto Fiorentino (FI)
Tel: +39 055 4574 243
Web: http://www.cerm.unifi.it/home
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Received on Mon Sep 20 2010 - 11:00:06 PDT
