[gmx-users] Re: Simulating a large system

[Dr. Vitaly Chaban]

If you do not care about the atoms, which are too far away from the region
of interest, is it not reasonable just to cut that "useless" part? Also,
you may want to look towards implicit solvent simulations.

Dr. Vitaly Chaban


On Mon, Apr 8, 2013 at 11:35 AM, Juan Antonio Raygoza Garay <
raygozag at psu.edu> wrote:

> Sure, it's basically improving minimization time. if i can focus all my
> resources in simulating or minimizing a portion of the system while
> ignoring other parts that are too far away from the selected portion, it
> can also be possible to run some simulations without the need of a big
> cluster and sort of obtaining about the same results. This goes to my
> interest of harnessing small computing systems for doing all these tasks.
> There are systems like rna molecules where i could get the fine grained
> structure first and then running the entire molecule to obtain the coarser
> structure.
>
> As someone says it might not improve time but at least having the ability
> to run portions only on my small desktop overnight or just leave it there
> running a lot of this could be accomplished. I do have access to a cluster
> but having to wait in the queue is time that can be used to getting
> somewhere, maybe slower but you're moving.
>
>
> On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote:
>
> Vitaly Chaban
>
>
>