Re: Acceptable Timescale fro NAMD

From: Oscar Bastidas (obastida_at_umn.edu)
Date: Wed Jul 24 2019 - 13:49:34 CDT

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.

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
>>
>

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