[gmx-users] Longer scale simulations

[Tsjerk Wassenaar]

Hi,

Depending on the geometry of your system and the flexibility, it can be 
worth performing the simulation in a molecular shaped box. This may save 
you 50% on computational time. If you like you can contact me off the list.

You will need a modified version of Gromacs though. I hope these 
roto-translational constraints make in into the next release :)

Greetings,

Tsjerk

Ran Friedman wrote:

> Well, that's not very encouraging, but it's better than being wrong!
>
> Thanks a lot,
> Ran.
>
> Berk Hess wrote:
>
>> >Does this approach still confer some advantages compared to normal MD?
>> >
>> >For example, can I use non-periodic boundary conditions in order to 
>> reduce
>> >computation time?
>>
>> No, it does not.
>> If you would want to use non-periodic boundary conditions you would 
>> need to
>> restrain the outer shell
>> of solvent atoms, which introduces artifacts. A boundary layer is 
>> required
>> to minimize the effect of
>> these artifacts.
>> In the end it is computationally cheaper to use a periodic system in a
>> rhombic dodecahedron box.
>>
>> Berk.
>>
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>-- 
>------------------------------------------------------
>Ran Friedman
>Laser laboratory for fast reactions in biology
>Department of biochemistry
>Faculty of life sciences
>Tel-Aviv university
>972-3-6409824
>------------------------------------------------------
>
>  



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