From: Monika Kumari (Monika.Kumari_at_chemistry.iitd.ac.in)
Date: Fri Oct 29 2021 - 23:43:56 CDT
Dear Dr. Giacomo
Thanks for the clarification regarding the deterministic simulations.
For the rattle error issue, I am loading the correct .colvars.state file.
The error most of the time disappears while using lower timesteps. Also,
this error is mainly encountered while running metadynamics on larger
molecules in a densely packed environment (e.g amino acid permeation in
lipid bilayer). I remember I never encountered the error while running a
metadynamics simulation of sodium ion passing through a pore.
Thanks.
On Fri, 29 Oct 2021 at 20:31, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hello Monika,
>
> On Fri, Oct 29, 2021 at 10:43 AM Monika Kumari <
> Monika.Kumari_at_chemistry.iitd.ac.in> wrote:
>
>> Dear all,
>> I am running a well-tempered metadynamics simulation with 2 fs timestep
>> using NAMD which is running fine but when I restart the run, it gives the
>> rattle algorithm error. What can the possible things I might be
>> overlooking. Please suggest.
>>
>
> If the instability is only at the restart, can you confirm that you are
> also loading the correct .colvars.state file alongside the correct NAMD
> coor/vel/xsc files?
>
> https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:colvars_input__;Iw!!DZ3fjg!uQUPilQRiRSQYJfoJoxMjUbrgPoBlRX3BmtRPnpaP9UAYVb1zRt2D9UC5NaGObuTbg$
> (If you used a NAMD patched with Plumed, you can follow the corresponding
> instructions for restarting).
>
>
>> Though after reducing the time step, the error disappears.
>>
>> Also, when I ran two simulations parallelly with exactly same files, the
>> colvar trajectory was different. Being molecular dynamics a deterministic
>> simulation, how could it happen?
>>
>
> This is false. Even with a completely deterministic set of options, the
> limited precision of floating-point math adds tiny errors that are
> completely harmless for the sake of physical accuracy but lead over time to
> diverging trajectories. And if you use a non-deterministic thermostat or
> barostat (very common in NAMD) determinism may go out the window from the
> very first step.
>
> Giacomo
>
>
>>
>> Thanks
>> Monika
>>
>
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