Hi,
In addition, the timestep of a simulation is determined by the so-called
Nyquist rate (information theory) which states that the sampling
frequency (the inverse of the timestep) should be at least twice the
highest frequency of your molecular system.
In practice, the highest frequencies are those involving X-H bonds (X
being any heavy atoms). They are related to the reduced mass and the
bond constant. This is why the usual timestep is about 0.5 to 1fs. By
applying SHAKE on X-H bond (ntc=2), you get ride of these frequencies,
but you are still limited by bond frequencies involving heavy atoms (all
C-C, C-N bonds, etc.). That's why people use timesteps around 1.5-2.0fs
with SHAKE. If you use a 5fs timestep on a typical biomolecular system:
1) your sample won't be correct; 2) you can (will!) blow your system up
since energy won't be conserved.
Finally, this is your system that governs your timestep. As stated by
Thomas, you will need to a clear justification why using such a timestep
if you're using it.
Gerald.
On 04/03/2013 09:43 AM, steinbrt.rci.rutgers.edu wrote:
> Hi,
>
> technically yes, but for typical molecular systems, the integrator would
> probably be way to coarse. So unless you can justify this very well for
> the system you look at, I wouldn't recommend it.
>
> Thomas
>
> On Wed, April 3, 2013 2:59 am, HM wrote:
>> Hi All,
>> Is it possible to have a time step of 5 fs in Amber ?
>>
>> Thanks,
>> HM
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
____________________________________________________________________________
Prof. Gerald MONARD
Theoretical Chemistry and Biochemistry Group
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Wed Apr 03 2013 - 01:30:03 PDT
