Re: Maximum Timestep for NAMD

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Feb 07 2019 - 15:37:58 CST

Is this what you mean?
https://www.ks.uiuc.edu/Research/namd/2.13/ug/node35.html#SECTION000103400000000000000

On Thu, Feb 7, 2019 at 4:36 PM Braden Kelly <bkelly08_at_uoguelph.ca> wrote:

> Has any thought been put into using multiple time step on the bonds rather
> than SHAKE?
>
> Braden
>
> Get Outlook for Android
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> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> *Sent:* Thursday, February 7, 2019 4:02:20 PM
> *To:* namd-l_at_ks.uiuc.edu; alexsaadfalcon_at_gmail.com; bennion1_at_llnl.gov
> *Subject:* RE: namd-l: Maximum Timestep for NAMD
>
> Yup. The 1-2 fs for atomic scale simulation comes from the fastest
> vibrational modes in the system. Bonds to hydrogen have oscillatory periods
> on the order of 10fs, with heavy atom bonds having periods that are only
> somewhat larger. In order to have your system not routinely blow itself
> apart, you need to keep your timestep somewhere between 8-10 times smaller
> than the vibrational periods in your system. This limits classical atomic
> simulations to 1fs. Unless you fix bond-lengths to hydrogen with
> SHAKE/RATTLE/LINCS, which will get you to 2fs. Or you can also restrain
> heavy-atom bond lengths and some angles, and get up to 4fs with virtual
> sites in gromacs. Coarse grained systems allow for larger timesteps because
> the particle masses are larger, and 20 fs timesteps aren't unheard of.
> Basically, if we could take 100fs timesteps without a loss in accuracy, we
> would already be doing it routinely. :)
>
> -Josh
>
>
>
> On 2019-02-07 13:49:27-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
>
> Hello,
>
>
>
> The first thing to consider is why the 1-2 fs timestep is most often
> used.
>
> You might also consider various accelerated MD methods and coarse grained
> MD.
>
>
>
> Brian
>
>
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> *On Behalf Of
> *Alex Saad-Falcon
> *Sent:* Thursday, February 7, 2019 12:25 PM
> *To:* namd-l_at_ks.uiuc.edu
> *Subject:* namd-l: Maximum Timestep for NAMD
>
>
>
> Hi all,
>
>
>
> What is the maximum acceptable timestep for NAMD? I would like to run
> longer (1ns to 1ms) simulations, and I am wondering how much I can increase
> the timestep (to 10fs or 100fs) without detracting terribly from accuracy--000000000000225f28058154aa4b--

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