[gmx-users] simulation acceleration of SWM4-NDP water and ions

[折晓会]

Thank you professor Justin! You are really professional. I will read the documents carefully.
Best wishes,Xiaohui
> Date: Sat, 15 Aug 2015 09:38:38 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] simulation acceleration of SWM4-NDP water and ions
> 
> 
> 
> On 8/15/15 9:13 AM, 折晓会 wrote:
> > Dear all,
> > I am using polarizable water model (SWM4-NDP) and ions in my simulation. However, the simulation speed is really slow, and it will take several days to get the simulation results.
> > I know the SWM4-NDP only supports 1 MPI thread at the moment. I am wondering if SWM4-NDP supports GPU acceleration, or is there other method to improve the simulation speed? I plan to upgrade my current workstation to speed up the simulation.
> > Any help will be appreciated!
> 
> Please see http://dx.doi.org/10.1002/jcc.23937
> 
> As a result of that implementation, I also made SCF compatible with domain 
> decomposition, so it is much faster than it was before.  The extended Lagrangian 
> is 3x faster than the SCF, but only supports NVT at this point.
> 
> You can get the force field files and instructions for how to get the code from 
> http://mackerell.umaryland.edu/charmm_drude_ff.shtml
> 
> There are no tutorials available (lack of time), but for a simple system like 
> water and ions, the example inputs in the SI of the paper are all you should need.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
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