[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,
> gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users