From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jan 12 2015 - 04:44:58 CST
Hi Thomas,
I am not that familiar with the method, but I suspect you could implement
conformational flooding itself or a close variant thereof as a scripted
collective variable bias on "eigenvector" coordinates.
The closest algorithm that's already implemented is of course metadynamics.
Jerome
On 12 January 2015 at 11:32, Thomas Evangelidis <tevang3_at_gmail.com> wrote:
> 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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