Re: AW: Replica Exchange: Equilibrating at each temperature

From: Horia Jalily Hasani (
Date: Thu Jun 02 2016 - 10:59:56 CDT

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 <>

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:* [
<>] *Im Auftrag von *Horia Jalily Hasani
*Gesendet:* Dienstag, 31. Mai 2016 18:18
*An:*; Norman Geist <>
*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



On Tue, May 31, 2016 at 7:41 AM, Norman Geist <> wrote:

Btw. do you want to implement the TIGER2 REMD algo? I can supply the code
for this too.

Norman Geist

*Von:* [] *Im
Auftrag von *Norman Geist
*Gesendet:* Dienstag, 31. Mai 2016 11:25
*An:*; 'Horia Jalily Hasani' <>
*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:* [
<>] *Im Auftrag von *Horia Jalily Hasani
*Gesendet:* Montag, 30. Mai 2016 18:28
*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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