[gmx-developers] MC integrator

[David van der Spoel]

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?
> 
> Cheers!
> 
> /Erik
> 
> Andre Assunção S. T. Ribeiro skrev:
>> Dear Developers,
>>
>> I have been working on a Monte Carlo integrator for GROMACS for some
>> time. I have now finished a working version. It is still very crude,
>> only treats rigid body translation/rotation and performance could be
>> much better. I have adapted the code for parallel runs, but only with
>> particle decomposition. I have tested it using a box with SPC water in
>> both NVT and NPT ensembles and the results look fine. I would appreciate
>> if anyone could take a look at the code and help me test it and/or give
>> any suggestions.
>>
>> The code can be downloaded from:
>> git://github.com/aastr/GROMACS.git
>>
>>
>>
>> The following mdp file has been used for NPT jobs:
>>
>> title             =  mc
>> cpp               =  /usr/bin/cpp
>> coulombtype       =  PME
>> constraints       =  none
>> integrator        =  mc
>> dt                =  0.002
>> nsteps            =  50000000
>> nstlist           =  1
>> ns_type           =  grid
>> rlist             =  0.9
>> rcoulomb          =  0.9
>> rvdw              =  0.9
>> fourierspacing    =  0.12
>> fourier_nx        =  0
>> fourier_ny        =  0
>> fourier_nz        =  0
>> pme_order         =  6
>> ewald_rtol        =  1e-5
>> optimize_fft      =  yes
>> nstxout           = 1
>> nstenergy         = 1
>>
>> tcoupl                   = berendsen
>> tc_grps                  = sol
>> tau_t                    = 0.1
>> ref_t                    = 300
>>
>> Pcoupl = MC
>> ref_p = 1.0
>> pcoupltype = isotropic
>> tau_p = 0.5
>> compressibility = 4.5e-5
>>
>> ; MC stuff
>> delta_v = 0.05
>> delta_r = 0.012
>> delta_phi = 15.0
>> nst_p = 400
>>
>>
>> Best Regards,
>> Andre Ribeiro
>> UFRJ - Brazil
>>
>>
>>
>>
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>>   
> 
> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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