[gmx-users] simulated annealing mdp

[Lord RaviRaj ..]

On Tue, Jun 12, 2012 at 4:42 PM, rama david <ramadavidgroup at gmail.com>wrote:

> THANK YOU Justin,
>
>
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Hello Justin,

In the last message you said "SA protocol simply heats and cools water,
which I don't think accomplishes much".. can you suggest the other
paramaters that must be  used  achieve, lets say the proper folding of
loops in a GPCR.





Secondly.,,In temperature coupling he  used 310 for the non protein system
and a range of temeratures from 310-323-310 for simulated aneealing.. how
the program treats the couling temperatures  and annealing temperatures
(310 and 310-323-310)..
Can you explain what temperature is applied to what groups in simple
membrane system with a GPCR system..

; Temperature coupling is on
tc-grps        = Protein Non-Protein    ; two coupling groups - more
accurate
ref_t        = 310     310    ; reference temperature, one for each group,
in K
;sim anealing
annealing_time          =  0  200  400 600 0 200 400 600
annealing_temp          = 310 323 300 310  310 323 300 310 .

'(Sorry if it feels like a premature question.. But I'm a beginner )
Thanks

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