Re: Reducing the system size

From: René Hafner TUK (
Date: Mon Aug 02 2021 - 16:37:12 CDT


    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
    (;!!DZ3fjg!pfngaJtp-At6padjIqr91VOvRvs4s5hQDu-QATgK7h16ugElye7icdVP_-QNdX78bA$ ) & (e.g.
    checkout previous post for hints,

      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 (

         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



On 8/2/2021 11:15 PM, ashkan shekaari wrote:
> No way.
> On Aug 2, 2021 7:29 PM, Ruturaj warake <> 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

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