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Feature #1627

DPD integrator

Added by Berk Hess about 5 years ago. Updated over 3 years ago.

Status:
In Progress
Priority:
Normal
Assignee:
-
Category:
mdrun
Target version:
-
Difficulty:
uncategorized
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Description

The MD group in Groningen has developed a DPD integrator with nice properties, which we would like to include in the Gromacs distribution.

There is a basic version, but some work needs to be done to make it work with MPI, (OpenMP) threads, the Verlet cut-off scheme and constraints.
I am not up to date on the details of the integrator. Nicu, could you post a link to the manuscript describing the integrator?

I assume the integrator should randomly pick a fraction of the pairs to act on. Then we need an mdp parameter to set this and then loop over the complete nbnxn pairlist (multi-threaded) and select pairs using a random number generator. All our other stochastic integrators now produce reproducible dynamics, even when running on different numbers of ranks and/or threads. It is going to be hard to achieve that for DPD. The only easy way I can see to achieve this is to use a random number for each particle pair, which is going to be very expensive when the probability of taking a pair is set low.

proof.pdf (645 KB) proof.pdf Second DPD article on contraints Nicolae goga, 10/17/2014 05:11 PM

Related issues

Related to GROMACS - Feature #1885: DPD ThermostatNew

History

#1 Updated by Nicolae goga about 5 years ago

Thanks Berk,

Here is the link to the article:

http://gbb.eldoc.ub.rug.nl/FILES/root/2012/JChemThCompGoga/2012JChemTheoryComputGoga.pdf

Constraints had a problem. Therefore a second article was written and published quite recentely. Attached here as a file.

Keep in touch
Nicu

#2 Updated by Mark Abraham over 4 years ago

  • Target version changed from 5.1 to 5.x

#3 Updated by Mark Abraham over 3 years ago

  • Target version deleted (5.x)

#4 Updated by Mark Abraham 11 months ago

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