> On Feb 5, 2015, at 1:44 PM, Hadeer ELHabashy <hadeer.elhabashi.gmail.com> wrote:
>
> Dear sir
>
> wish you are fine !
> Thanks for your response !
> Actually, I used to write the control files like this because it is similar
> to that printed in the output file of AMBER. However I've tried to simplify
> them as possible as I can. so you can check them and comment easily.
> Also, I was using nsnb=1 with ntb=1 only to remove the rotational and
> transnational center of mass each step.
nsnb is an outdated option dictating how frequently pairlist rebuilds are done. It has nothing to do with COM removal (that is nscm).
> I know it is costly ! However, I am
> planning to increase it upto 500 or remove it from the control file.
> I am using force field of ff99 and the water model is TIP3PBOX.
ff99 is 15+ years old, and has many well-known deficiencies that have been addressed in newer force fields. You choice of force field is MUCH more important than whether you remove COM motion every 1 or 500 steps, or whether you use SHAKE or not. I suggest you look at the discussion on force fields in the Amber14 manual to help inform which choice you should make.
> The
> conformational changes happened are favorable, expected and reasonable.
> but I don't know if they are real time events or accelerated events. I
> want to be able to claim or propose that this protein will behave similarly
> in practical experiments.
Many things can affect kinetic measurements, and no simulation technique except for strict NVE can preserve temporal properties (i.e., the use of a thermostat or any stochastic dynamics model ruins the time-continuity of your trajectory). Instead, I would use these simulations to characterize the free energy surface and use that surface to say something about expected transition rates between different states (you can compare *that* back to experiment).
> What if I removed the shake from the production
> md, do think that may slow down this conformational changes I got.
No.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 05 2015 - 12:00:02 PST
