Re: is there a method equivalent to conformational flooding in NAMD 2.10

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Mon Jan 12 2015 - 04:32:17 CST

​Hi Norman,

You forget that this is a transmembrane protein and hence I can't raise the
temperature too much. In fact I can't even raise the aMD boost too much
because the membrane bilayers dissociate. And yes, I am pretty sure about
my aMD setting, I 've experimented a lot with them. As for REMD, it is out
of option. It requires many replicas to maintain a reasonable exchange rate
for a protein of 429 amino acids, even in the Hamiltonian-REX variant. What
I had in mind when I posted the question was some method that utilizes the
collective variable modules of NAND and/or its Tcl scripting interface.

Thomas

On 12 January 2015 at 08:53, Norman Geist <norman.geist_at_uni-greifswald.de>
wrote:

> Hi,
>
>
>
> well you are likely caught in a deep minimum, which actually could be the
> global one aswell, doesn’t it? Either this would explain why nothing
> happens, or if you think there should be happening something, you’d like to
> put more energy into the system to actually allow conformational changes
> and crossing energy barriers. At which temperature did you run this 1µs? I
> think you could try to run a usual MD at a higher temperature, but not high
> enough to cause complete unfolding. Another option might be a REMD with
> lower Tmax to do the same.
>
>
> ​​
>
> Also, are you sure that your settings for the aMD were suitable? Maybe
> you can post them here along with some details about the size of the
> protein and so someone can share some opinions about it.
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Thomas Evangelidis
> *Gesendet:* Sonntag, 11. Januar 2015 14:44
> *An:* namd-l
> *Betreff:* namd-l: is there a method equivalent to conformational
> flooding in NAMD 2.10
>
>
>
>
>
> Dear NAMD list,
>
> Is there any method in NAMD equivalent to Helmut Grubmuller's
> Conformational Flooding? I want to open a transporter starting from an
> intermediate state in which it was crystallized, but I don't know the final
> state. So far, I have ran a 1 microsecond aMD simulation but nothing
> happened. I conducted all my simulations with NAMD hence I hesitate
> migrating to GROMACS.
>
> thanks,
> Thomas
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang_at_pharm.uoa.gr
>
> tevang3_at_gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
> ===============================================================
>
> *Physics is the only real science. The rest are just stamp collecting.*
>
> *- Ernest Rutherford*
>

-- 
==================================
​sdfwf​
====================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
===============================================================
*Physics is the only real science. The rest are just stamp collecting.*
*- Ernest Rutherford*

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