Re: Replica Exchange: Equilibrating at each temperature

From: Horia Jalily Hasani (jalilyha_at_ualberta.ca)
Date: Tue May 31 2016 - 11:18:08 CDT

Hi Norman,

Thanks for your response. The reason I wish to equilibrate the system at
each temperature is because it contains lipids and abrupt temperature
changes destroy the bilayer. Would minimization help in this regard or do
you have any other suggestions?

P.S. I'd appreciate if you could provide me with the modified code you
mentioned.

Regards,
Horia

On Tue, May 31, 2016 at 7:41 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Btw. do you want to implement the TIGER2 REMD algo? I can supply the code
> for this too.
>
>
>
> Norman Geist
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Norman Geist
> *Gesendet:* Dienstag, 31. Mai 2016 11:25
> *An:* namd-l_at_ks.uiuc.edu; 'Horia Jalily Hasani' <jalilyha_at_ualberta.ca>
> *Betreff:* AW: namd-l: Replica Exchange: Equilibrating at each temperature
>
>
>
>
>
> Doing an equilibration doesn’t make sense in a REMD at all, since it’s its
> aim to be independent of the starting structure. What you can do to set up
> REMD simulations easier without need to prepare the systems, is to add a
> minimization to each replica. This would need to be implemented in
> replica.namd. But you should rotate the DCDfile option before minimization,
> and afterwards back to the production name in order to not have the
> minimization frames in the normal DCDs since this will mess up sortreplicas
> and the history files.
>
>
>
> I’ve done this already and can supply you the code changes necessary ;)
>
>
>
> Norman Geist
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu
> <owner-namd-l_at_ks.uiuc.edu>] *Im Auftrag von *Horia Jalily Hasani
> *Gesendet:* Montag, 30. Mai 2016 18:28
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: Replica Exchange: Equilibrating at each temperature
>
>
>
> Hi,
>
>
>
> I wish to implement a step during REMD, to equilibrate each replica at its
> own temperature before starting the swaps.
>
>
>
> Considering I have the following 3 files, I am not sure which one should
> be modified and how should it be done:
>
> replica.conf
>
> _base.namd
>
> replica.namd
>
>
>
> Your response is much appreciated.
>
>
>
> Regards,
>
> Horia
>

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