From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Mon May 08 2006 - 17:38:07 CDT
Hi all, thanks for all the replies. Himanshu mentioned that SHAKE/RATTLE algorithem, which is probably set in Charmm program.
I am using NAMD now, and is the keywork "rigidbonds" aimed at fixing the streching mode of hydrogen atoms?
Thanks for your time.
Boyang.
Himanshu Khandelia <hkhandel_at_dtc.umn.edu> £º Boyang,
2 fs is the timestep you MUST use, for an all-atomistic system, as long as
you are using the SHAKE/RATTLE algorithm to constrain the hydrogens.
Longer than 2 fs timesteps lead to instabilities, unless you are using the
multiple-time step algorithm. Smaller steps will be inefficient. 2 fs is
optimally correct.
Yes, you can use the 2 fs for a 50ns simulation. Why not ?
-himanshu
On Tue, 9 May 2006, Boyang Wang wrote:
> Hi all. I am again asking something related to the timesteps in NAMD.
>
> As stated in many molecular dynamics methods, the time step should be about one order of magnitude smaller than the fastest motion in the system we simulate.
>
> In a typical chemical or biological system, the fastest motion, O --- H bond streching, or N -- H bond streching, has a period of about 12 fs, according to the force constant of OT--HT bond in the Charmm force field.
>
> Therefore, it seems OK to me if I apply a timestep of 2 fs in the simulation of a chemical system.
>
> Could anybody who is familiar in this topic give me some hint? Thanks for your time.
>
> Sincerely,
>
> Boyang.
>
>
> Boyang Wang,
> Email - bwang9_at_uic.edu
> Major - Phys. Chem.
> dept Chemistry,
> Univ Illinois, Chicago,
> 60607 IL US.
>
> ---------------------------------
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