From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 02 2016 - 01:33:55 CDT
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?
Von: owner-namd-l_at_ks.uiuc.edu [mailto: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
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.
On Tue, May 31, 2016 at 7:41 AM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto: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.
Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto: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 <mailto:namd-l_at_ks.uiuc.edu> ; 'Horia Jalily Hasani' <jalilyha_at_ualberta.ca <mailto: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 ;)
Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto: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 <mailto:namd-l_at_ks.uiuc.edu>
Betreff: namd-l: Replica Exchange: Equilibrating at each temperature
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:
Your response is much appreciated.
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