Re: Acceptable Timescale fro NAMD

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jul 24 2019 - 14:22:32 CDT

On Wed, Jul 24, 2019 at 2:52 PM Oscar Bastidas <obastida_at_umn.edu> wrote:

> For rhis particular question, I am not looking at a particular system with
> specific parameters (i.e. number of atoms). I just want to guage
> what the limitations are for namd, generally speaking. Obviously, nothing
> below femtoseconds will do on account of the integrator time step. By a
> similar guage, is there a cut-off for when NAMD alone (without advanced
> tricks like enhanced sampling) ceases to provide information on protein
> behavior. If hundreds of nanoseconds is a reasonable max that's been
> used/published then that answers my question for that upper limit. Thanks.
>

it doesn't matter that *you* are not looking at a particular system. there
is no such system independent value. it *really* all depends on the size
and type of system and the property under investigation. for the same
system, in some cases, a few hundred picoseconds can be sufficient and in
other cases even milliseconds would not be enough. there is no
one-size-fits-all solution. sorry.

axel.

>
> Oscar
>
> Oscar Bastidas, Ph.D.
> Postdoctoral Research Associate
> University of Minnesota
>
> On Wed, Jul 24, 2019, 1:21 PM Bassam Haddad <bhaddad_at_pdx.edu> wrote:
>
>> It largely depends on the question you are asking. What are the
>> timescales that the phenomenon occurs? How do you plan on monitoring
>> convergence to equilibrium? I have published work with a total of 1.4 us of
>> simulation, however, no single system had more than 300 or 400 ns.
>>
>> Bassam
>>
>> On Wed, Jul 24, 2019 at 10:39 AM Oscar Bastidas <obastida_at_umn.edu> wrote:
>>
>>> Hello,
>>>
>>> Would someone please tell me what is an acceptable time window (i.e.
>>> single femtoseconds to 100s of nanoseconds) that the community accepts for
>>> using NAMD to conduct simulations? If you have a reference, all the
>>> better. Thanks.
>>>
>>> Oscar
>>>
>>> Oscar Bastidas, Ph.D.
>>> Postdoctoral Research Associate
>>> University of Minnesota
>>>
>>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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