Application Information

This project made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1)

For work done after 01/01/2023:

This project made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/X035603/1)

Research Themes

We are collecting information as to whether a given project aligns against a number of our current research themes. We would encourage applicants to indicate the correct theme/s for their project proposal, projects that align against these themes may be looked on as more desireable. Our current research themes are:

Antimicrobial Resistance.
Biomolecular design for synthetic biology, future health care and industry.
Simulation for drug discovery.
Understanding the molecular origins of disease.
Pushing the boundaries of biomolecular simulation.
Multiscale modelling of biomolecular systems.
Directed and self-assembly

Allocation Periods

The following allocation period dates are the date ranges in which you will be able to get physical access to different HPC facilities via HECBioSim to make use of your resource allocation awarded. Note, that these dates are different to the panel deadline dates in which you should have made your application, the call to the panel will normally open 1 month prior to the allocation window starting.

Allocation Period 1: 01/01/2023 - 30/06/2023
Allocation Period 2: 01/07/2023 - 31/12/2023
Allocation Period 3: 01/01/2024 - 30/06/2024
Allocation Period 4: 01/07/2024 - 31/12/2024

How to Apply

There are two main channels for getting time via HECBioSim. These are the smaller pilot type projects where you are wanting to try a new method, code or test a new architecture. Or there is a standard projects application that will go via peer review at a Resource Allocation Panel.

Pump-Priming Project

For a Pump-Priming project, on any of the machines that HECBioSim grants access to, you should contact This email address is being protected from spambots. You need JavaScript enabled to view it. to discuss your project needs with us.

Standard RAP

In order to apply for HECBioSim time on any of the UK HPC resources that we run calls for we will open up calls for access to HPC around 1 month before an allocation window begins. You should prepare a scientific technical case as instructed below and then complete an application for access during the application window. We will advertise our call open dates on this page, and also on the twitter account and CCPBioSim mailing list. Please note, we support access using the following software packages:

AMBER
GROMACS
LAMMPS
NAMD

The following table gives some outline simulation ranges per code for an illustrative set of simulation sizes. Please note that the ranges are in microseconds of simulation, and form a guideline only to provide ball-park ranges for how you will be assessed. This means that you simply add up all of your simulations (including replicas, repeats etc) lengths in microseconds and they can fall within these ranges where the panel will consider them as a standard sized project or a large project and apply assessment accordingly. This means that you are no longer are required as part of the application process to go to the extra step of then working out the conversion to compute units as in previous rounds.

	AMBER 18 - 22 (µs)		GROMACS 2021 - 2023 (µs)		NAMD 2.x (µs)		NAMD 3.x (µs)
atom count	std range	large	std range	large	std range	large	std range	large
20,000	305 - 490	550+	365 - 670	730+	140 - 280	300+	132 - 210	230+
61,000	175 - 280	316+	160 - 301	325+	50 - 105	110+	93 - 150	165+
465,000	25 - 40	45+	18 - 31	34+	7.0 - 14	15+	10.0 - 16	18+
1,400,000	7.5 - 12	14+	7.8 - 14	15+	2.3 - 4.7	5+	3.3 - 5.3	6+
3,000,000	3.4 - 5.5	6+	3.5 - 6.4	7+	0.8 - 1.7	1.8+	1.5 - 2.4	2.7+

Advice for Application Justification Document

This advice is aimed to help improve the quality of applications and help to level the playing field between more established groups and those that are new to our community. These guidelines aim to show some of the characteristics that all strong applications have in common whilst addressing some of the common questions we are asked. The justification document should be made up of two main parts, with the science case forming the bulk of it and the technical case to show a breakdown of how the resources are to be used.

Scientific Case

You should explain the science behind the study you are applying for HPC time for. This should include a brief overview of the aims of the project, what you will be studying and what the expected impact of this study would be, we would encourage you to use imagery and to summarise any preliminary work to help justify your case. If you are working in very sensitive areas, and cannot for various reasons include some details in your application, this does not mean you are excluded from applying but we would ask you to get in touch so that we can advise on how best to approach this document.

Technical Case

In order to stand a good chance of success, we strongly require that you detail the simulations you are doing. This should include information on the software package and methods you are aiming to use in your simulations. The best and clearest way of detailing simulations is to tabulate them by simulated system size (number of atoms) and provide information on simulation time and any number of repeat runs. This is important because the panel will use this information to place your project on the optimum HPC platform, and to calculate the size of allocation required to do your project.

You can increase your chances of obtaining at least some allocation by providing a reduction scenario. These panels are often oversubscribed, sometimes by nearly 2X the amount of resource we can allocate. Our panels are usually in a position where they are considering reduction scenarios, which can include allocation on a different resource or to cut the time given or to reject the case entirely. It often makes this process better for the applicant and the panel if reductions can be done in a way that is not detrimental to the study, ie that at least some progress can be made and potentially realise some outputs. Itemising as suggested above is one natural way to do this as you can then simply suggest a priority or a minimum as to what could be done under a reduction scenario. Another is if you could reduce the lengths or numbers of replicas etc.

FAQs

We will add answers to questions that are most commonly sent to us here.

Can PhD's/PDRA's apply as a PI?

In short, no. The PI must be a permanent member of academic staff affiliated to a UK institution. Proposals sent by PhD students or post doctoral researchers will be rejected.

Can researchers overseas be listed as a project user?

No, users can be of any nationality but must be working/studying at a UK institution.

Can purely industrial projects apply for time?

We are unable to offer time directly to industrial projects, nor can we sell access or act as a commercial service provider. We do however welcome applications from collaborative projects between academic and industrial parties, often such projects will be ranked highly due to having an industrial collaborator. These collaborations are highly encouraged, do not require financial contribution from the industrial partner and can be quite broad in scope (methods development, test applications, studentships, code development, to try out ideas, etc).

How long can a project last?

A project via HECBioSim can last no longer than 6 months.

Why do projects that use certain codes not require an ARCHER2 technical assessment?

The ARCHER2 technical assessment process is designed to ensure that codes are used effectively on this resource (scaling, job sizes and durations, etc.). In the case of the common MD codes, being used in “standard” ways, the consortium has sufficient existing knowledge of their performance to be able to by-pass this step. The current list of software that does not require you to get an ARCHER2 technical assessment is:

GROMACS
LAMMPS
NAMD

Should you feel that you know of software that should appear on that list then please get in touch and explain why you think it should be on the list. It may arise that the consortium could utilise your knowledge/expertise with such software such that we can broaden our support for software.

Why was my application rejected based on a previous project containing unused resource allocation?

New project applications from applicants that have had previously successful applications and then subsequently went on to under use their allocation by 50% and upwards at the time the project closed, will be looked at. Project applications that fall into this category will likely be heavily penalised during the panel review.

What are my options if my application is rejected?

Unfortunately due to the limited amount of compute time at each HECBioSim panel and the high volume of applications for HECBioSim time on HPC, it is not always possible to accept every single application. If your application is rejected then your options include but are not limited to:

Submit another application to HECBioSim for the next decision panel (it will be subject to the same review process).
You can apply for various types of access to ARCHER2 directly from the ARCHER2 website.
If your institution is a partner on one of the Tier2 facilities then you could apply through your local contact if they have capacity to offer this.

Why have I only been credited half of my award?

We typically do this on the machines that are shared by many communities, user groups and research councils. This is because what typically happens is that we see a lot of congestion towards the end of an allocation period and jobs can't be run due to all users groups having to use their resource at the same time. To prevent this happening, we run active profiling of the resource use, and we require you to burn the first half of your time both before the half way point in the allocation period and in order to release the second half. For the worst offenders, the second half may be reprofiled if use is poor.

What time on deadline day will applications close?

We will always have the application form set to close at 17:00 (GMT) on the day of the application deadline, this is inline with UK business hours. The form link will disappear precisely at 17:00 and applications already underway will not be able to be submitted past 17:00, it is strongly advised to complete your application in the weeks that is open.