Re: [gmx-users] can we use large timestep for membrane GPU simulation?

2013-04-28 Thread Justin Lemkul 



On 4/28/13 6:15 AM, Albert wrote:

Hello:

  I am watching Eric online Gromacs GPU webminar these days. I notice that he
talked about introduce large timestep (5fs) for GPU simulations on a water
system. I am just wondering, can  we also introduce such big time step for
membrane system if we are going to run the job in Gromacs?



The key to using a 5-fs timestep is constraining all bonds and using virtual 
sites.  If you do this, you can use such a timestep with just about any system.



What's more, Eric also shown the GLIC ion channel simulation with 150,000 atoms.
E5-2690+GTX Titan can get up to 38ns/day. But he didn't talked about what's the
timestep and cutoff.



Can't comment on this part.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] can we use large timestep for membrane GPU simulation?

2013-04-28 Thread Albert 

Hello:

 I am watching Eric online Gromacs GPU webminar these days. I notice 
that he talked about introduce large timestep (5fs) for GPU simulations 
on a water system. I am just wondering, can  we also introduce such big 
time step for membrane system if we are going to run the job in Gromacs?


What's more, Eric also shown the GLIC ion channel simulation with 
150,000 atoms. E5-2690+GTX Titan can get up to 38ns/day. But he didn't 
talked about what's the timestep and cutoff.


could anybody comment on this?

thank you very much
best
Albert
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