Re: Acceptable Timescale fro NAMD

From: Oscar Bastidas (obastida_at_umn.edu)
Date: Wed Jul 24 2019 - 14:32:03 CDT

That's fine. Thanks.

Respectfully submitted,

Oscar

Oscar Bastidas, Ph.D.
Postdoctoral Research Associate
University of Minnesota

On Wed, Jul 24, 2019, 2:22 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> 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.
>

This archive was generated by hypermail 2.1.6 : Thu Dec 05 2019 - 23:20:48 CST