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Feature #3285

Feature #3283: Support for the string method with swarms of trajectories in GROMACS

Run simulations from the same tpr file with different random seeds

Added by Oliver Fleetwood about 2 months ago. Updated 25 days ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
mdrun
Target version:
Difficulty:
simple
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Description

In e.g. the swarms of trajectories methods (see https://redmine.gromacs.org/issues/3283) one wants to start many short simulations from the same initial tpr file. Unless you use mdrun with the '-multi' option this is not possible and you need to create one tpr file per short trajectory, which is unnecessary.
A nice solution would be to reseed via a flag to mdrun.


Subtasks

Task #3356: Expose setting of random seed to APINew

Related issues

Related to GROMACS - Feature #3295: Expand gmxapi.modify_input use cases.New

History

#1 Updated by Mark Abraham about 2 months ago

  • Parent task set to #3283

#2 Updated by Eric Irrgang about 2 months ago

It is increasingly beyond the scope of mdrun functionality to alter simulation inputs in the same command. It would seem reasonable to expand convert-tpr to edit additional trivial properties, like random number seeds. This is also the purpose of the gmxapi.modify_input operation. However, neither of these options currently avoids the need to write a new TPR file. I think that an API abstraction for the simulation input will be a high priority for near term development.

#3 Updated by Eric Irrgang about 1 month ago

Oliver Fleetwood wrote:

A nice solution would be to reseed via a flag to mdrun.

There are several places where random number seeds can appear in a GROMACS simulation work flow, and the (re)use of explicit or automatically generated seeds can drift over time...

Can you please clarify which random process(es) you would like to reseed?

#4 Updated by Eric Irrgang about 1 month ago

  • Related to Feature #3295: Expand gmxapi.modify_input use cases. added

#5 Updated by Paul Bauer 30 days ago

The new feature here would likely be mostly useful for re-seeding the velocity generation to be able to generate the trajectory swarms with different initial conditions.

I think this would be a prime example of using the API to create input diversity without having to generate different input files, or having to use an unrelated feature (multisim) to get the same result.

#6 Updated by Eric Irrgang 25 days ago

Paul Bauer wrote:

The new feature here would likely be mostly useful for re-seeding the velocity generation to be able to generate the trajectory swarms with different initial conditions.

If this is correct, then I suggest updating the issue title to be more explicit. E.g. "with differently seeded random initial velocities"

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