From: Horia Jalily Hasani (jalilyha_at_ualberta.ca)
Date: Tue Jun 07 2016 - 11:21:09 CDT
Hi Norman,
Thanks for the tips. These would definitely help.
Regards,
Horia
On Fri, Jun 3, 2016 at 12:39 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Ok, but does the membrane survive the high temperatures? Otherwise you
> should consider fixing some of the lipid atoms so the membrane will stay as
> is. While the protein is free to move. You should also consider fixing or
> constraining parts of the protein you don’t want to unfold due the higher
> temperatures.
>
>
>
> Norman Geist
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Horia Jalily Hasani
> *Gesendet:* Donnerstag, 2. Juni 2016 18:00
> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Cc:* <namd-l_at_ks.uiuc.edu> <namd-l_at_ks.uiuc.edu>
> *Betreff:* Re: AW: namd-l: Replica Exchange: Equilibrating at each
> temperature
>
>
>
> I have a small membrane protein for some parts of which I wish to see the
> changes in secondary structure and possible conformations in the presence
> of lipid.
>
>
> On Jun 2, 2016, at 12:33 AM, Norman Geist <norman.geist_at_uni-greifswald.de>
> wrote:
>
> No the minimization was just something I implemented in my replica.namd so
> I don’t need a extra run to prepare new REMD simulation.
>
>
>
> In your case, I don’t know if it makes sense to perform a replica exchange
> md on a structure that will not survive the high temperatures. Can you
> explain what else is in your system and what is the purpose of your REMD?
>
>
>
> 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:* Dienstag, 31. Mai 2016 18:18
> *An:* namd-l_at_ks.uiuc.edu; Norman Geist <norman.geist_at_uni-greifswald.de>
> *Betreff:* Re: namd-l: Replica Exchange: Equilibrating at each temperature
>
>
>
> 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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