From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Mon Aug 02 2021 - 16:37:12 CDT
Hi
it mainly depends on what you simulate.
One things the (water) solvation layers you add to your system in z
and xy directions respectively.
In case of membranes you might just build a smaller one (at least in
XY plane of membrane bc this can also drastically reduce the
solvation layer volume size).
One further option is you might check out if HMR
(https://urldefense.com/v3/__https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00160__;!!DZ3fjg!pfngaJtp-At6padjIqr91VOvRvs4s5hQDu-QATgK7h16ugElye7icdVP_-QNdX78bA$ ) & (e.g.
checkout previous post for hints,
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/1555.html)
This basically makes all non-solvent hydrogens heavier (and
connected heavy atoms lighter) and one can increase timestep to 4fs
(with nbbonded and fullelect set to one 2).
For standard mass and case I use the timestepping scheme of 2-1-2.
And last but not least if you do not need any special things but
have a somewhat recent GPU at hand you may wanna try out
NAMD3.0alpha (http://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/)
This helped me a lot too in a rather simple
equilibration/stability check for longer simulations.
For any further guidance, as always, one needs to provide more
information.
Regards
René
On 8/2/2021 11:15 PM, ashkan shekaari wrote:
> No way.
>
> On Aug 2, 2021 7:29 PM, Ruturaj warake <ruturajwarake47_at_gmail.com> wrote:
>
> Dear Users,
> I am running simulation for 100ns. But due to large system size,
> it's taking lot of time to run the simulation. So I need to reduce
> the system size.
> How can I reduce it ? Please help me out.
>
> Mr. Ruturaj Warake
> Niper, Hyderabad
> India
>
>
-- -- Dipl.-Phys. René Hafner TU Kaiserslautern Germany
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