[gmx-users] simulated annealing mdp

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 12 14:33:46 CEST 2012

On 6/12/12 8:20 AM, Lord RaviRaj .. wrote:
> On Tue, Jun 12, 2012 at 4:42 PM, rama david <ramadavidgroup at gmail.com
> <mailto: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.

I should clarify that - the SA protocol does indeed heat and cool the protein as 
well, but accomplishes nothing because restraints were applied.

To refine loops, don't use restraints.  One can create a custom posre.itp file 
with genrestr to restrain some parts of a protein (i.e., well-folded secondary 
structure elements) while letting others move.  This may be necessary if using 
high temperatures that would otherwise cause the protein to unfold.  Restraints 
can be useful, if applied appropriately.

> 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..

Temperatures are scaled linearly between the values listed in annealing_temp 
over the times set in annealing_time.  The values set for ref_t are irrelevant, 
but one does need to set appropriate values for other temperature coupling 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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