Aw: [gmx-users] Re: Simulating a large system

2013-04-08 Thread lloyd riggs
 [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

Re: [gmx-users] Re: Simulating a large system

2013-04-08 Thread Mark Abraham
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

Re: [gmx-users] Re: Simulating a large system

2013-04-08 Thread Justin Lemkul
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

[gmx-users] Re: Simulating a large system

2013-04-08 Thread 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 < raygo...@

[gmx-users] Re: Simulating a large system

2013-04-08 Thread Juan Antonio Raygoza Garay
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

[gmx-users] Re: Simulating a large system

2013-04-08 Thread Dr. Vitaly Chaban
> 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