Re: [AMBER] GRID-enabled web portal for the use of the AMBER

From: Lucio Ferella <>
Date: Thu, 16 Dec 2010 14:05:25 +0100

> 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?

Hello Sergio,
thank you for you message and sorry for the late reply.
Unfortunately the web portal can't be exported to another location
because it was bound to the e-NMR European project and now it has been
inherited by the We-NMR European project. We are however studying
possible solutions that go in this direction, which might imply the
payment of a fee (the European Union asks us to try and make some money
out of our work...).
I agree with you when you say "MD can run for weeks to months, depending
on the system under study". Nevertherless, it is still possible to do
this by using our computational infrastructure. To this end, you can
use our Amber web GUI, which now includes a specific GUI to restart MD
jobs. In this way, you can run your (very) long MD in various blocks,
each lasting some days (we are not bound to the time limies of SBGrid),
by restarting it after each slot finishes. Maybe this is not the best
solution, but it can help.

Please let me know if you think that this solution might be feasible
Best regards

> -----Original Message-----
> From: Lucio Ferella []
> Sent: Monday, September 20, 2010 5:11 AM
> To:
> 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:
> -
> OR
> - (and clicking on<AMBER> menu item)
> Sincerely,
> Lucio Ferella

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Received on Thu Dec 16 2010 - 05:30:02 PST
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