From: Braden Kelly (bkelly08_at_uoguelph.ca)
Date: Thu Feb 07 2019 - 15:34:48 CST
Has any thought been put into using multiple time step on the bonds rather than SHAKE?
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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. :)
On 2019-02-07 13:49:27-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
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.
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
Subject: namd-l: Maximum Timestep for NAMD
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. What do I need to consider?
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