Dear Dr. Simmerling
Thank you for your reply,
HMR or virtual sites definitely allow 4fs, however, my question is about "classical MD". I ran MD with simple h-bonds constraints and 2.5 fs time step, the results of the simulation, including energies of the system were similar. I am curious we use 2 fs if there is no difference? Or there are pitfalls I have not noticed?
All the best,
Harutyun
> Date: Mon, 19 Apr 2021 09:02:59 -0400
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] 2.5 fs integration time step
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGk3s-SLR7c-sz9d8zK0Dh39pdimt=EpfD6PWeFxgjSE3VJXkQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> if you use hydrogen mass repartitioning (in parmed) then you should be able
> to use a 4fs time step, we do this for most of our simulations.
> https://pubs.acs.org/doi/10.1021/ct5010406
>
> On Mon, Apr 19, 2021 at 8:49 AM <h_sahakyan.mb.sci.am> wrote:
>
>> Dear Colleagues,
>>
>> Some researchers use the 2.5 fs integration time step, an example
>> is this work How Fast-Folding Proteins Fold | Science (
>> https://science.sciencemag.org/content/334/6055/517/tab-article-info). Do
>> you have any ideas on how 2.5 fs can affect MD simulations?
>>
>> All the best,
>> Harutyun Sahakyan
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Received on Mon Apr 19 2021 - 23:30:02 PDT
