[gmx-developers] MC integrator

[Erik Marklund]

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.

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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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys