[gmx-developers] MC integrator

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 6 08:07:59 CEST 2009

David van der Spoel wrote:
> Erik Marklund wrote:
>> Swell! It's been missing from gromacs for a long time in my oppinion.
>> Regarding parallelism, MC is highly parallelizable in "step-space", 
>> and computing different MC steps on different processors will most 
>> likely be faster than distributing particles or domains, since 
>> virtually nothing needs to be communicated. Therefore, a 
>> step-decomposition option is a good idea. Plus, it would be very easy 
>> to implement.
> This is not necessarily true if we move to many (tens of thousands of 
> processors) which soon will be feasible with gmx 4.1 once it is 
> finished. Hence I would prefer if the code did not "interfere" with the 
> parallellisation, but rather just uses the existing logic. Maybe I 
> misunderstand it, but you do a trial move and then recompute the energy, 
> right?

Reworking the multi-simulation feature that already exists would be the 
best of all worlds. In REMD you have a bunch of the same system in 
different states, which sometimes move, but in straight MC you can have 
many copies of the same system computing different trial moves. The 
catch is that when you accept a move, you probably have to throw away 
any work on the old state and communicate the successful move to all 
systems. Does that suggest constructing low-probability moves to 
minimise wastage? Dunno.


More information about the gromacs.org_gmx-developers mailing list