[gmx-users] Re: Folding rate

[bharat gupta]

Thanks for the reply. Since I need to study the effect of beta-hairpin turn
design on protein folding . I thought that first unfolding and then
refolding would give the change in folding time. As you told that to do
such a task would require large computational power. Is there any other
method in MDS that could be used ??

On Wed, Jan 4, 2012 at 10:52 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 4/01/2012 12:35 PM, bharat gupta wrote:
>
>> Thanks for all your replies. I want to know this can be done in gromacs
>> or not - using REMD with structure based models generated from SMOG server
>> to study protein folding and unfolding ??.
>>
>
> Well, it can be done, but you probably don't have enough computer to fold
> a 230 residue protein at atomistic resolution (or maybe even
> coarse-grained).
>
>
>  Also, I have a question about how to determine  the exchange probablities
>> for a particular REMD experiment and also how many replicas do we need to
>> consider, does that depend on the temperature list generated from the
>> T_REMD server??
>>
>
> There's a significant literature on these subjects. I suggest you read
> some of it. Short answer: pick the highest temperature according to the
> size of the largest barrier you expect to cross (good luck guessing that),
> have around 20% exchange acceptance, and be prepared to observe where the
> replica-flow bottle necks are and to iteratively refine you temperatures.
>
> Mark
>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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South Korea
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