[gmx-users] Re: Simulating a large system
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 simulati
Yes, there's no way to cheat on the explicit electrostatics to reduce cost,
except implicit solvation. The kind of approach used in QM/MM is not useful
for MM/MM! The rate-limiting part is still there.
Mark
On Apr 8, 2013 12:42 PM, "Justin Lemkul" wrote:
> On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vit
On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban wrote:
> 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,
>
Hear hear. If it's so meaningless, why is it there? ;)
> you may want to look toward
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 <
raygo...@
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
> Hi, is it possible to instruct gromacs to only perform the dynamics on
> half of the system or protein while ignoring the rest?
>
> thanks
>
Would you explain to us why you need so exotic setup?
Dr. Vitaly Chaban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mail
6 matches
Mail list logo
