[gmx-users] A favor question: experience running Gromacs in the cloud

Andrew DeYoung adeyoung at andrew.cmu.edu
Fri Oct 19 01:59:56 CEST 2012

Hi, Gromacs users,

If you have time, I am wondering if you have any advice, as a favor.

I'm a graduate student in computational chemistry in the U.S.  My department
has an EXCELLENT "in-house" cluster, on which I routinely run Gromacs jobs
on 8 to 24 cores.  However, it occasionally happens that I run into a
"crunch time" need for some more computational resources.  For example, I
recently found a mistake (an incorrect parameter) that I made in an .itp
file that I wrote.  This means that I need to rerun a whole slew of
simulations as quickly as possible so that I can continue on with the

I am interested in purchasing temporary computational resources for using
Gromacs.  Do any of you have experience running Gromacs "in the cloud" -- on
a service such as Amazon EC2 (http://aws.amazon.com/ec2/)?  For my quick
need for computational resources, some sort of cloud solution looks
interesting to me.  On the other hand, I could apply for time on XSEDE
(https://www.xsede.org/), but that would probably be a lengthier process,
and probably more suitable for a longterm solution. 

The problem with the cloud idea is that I am not an expert on computers and
networking, so I am worried that actually successfully using cluster time
might be difficult (whereas I have heard that, in contrast, Gromacs is
sometimes more or less pre-installed on university/national lab-based
supercomputer resources available through XSEDE grants).  Have you ever used
Gromacs on a cloud service? 

Thank you for your time! 

Andrew DeYoung
Carnegie Mellon University

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