On 8/6/13 2:45 PM, ypca wrote:
Thank you for the help!
I can completely understand you, but what about the simulated annealing,
isn't it automatically for all systems?
No. If you want to perform simulated annealing, use simulated annealing options
(see the manual).
Why the increase of temperature is so fast, like in lysozyme tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html)?
It's not an increase, per se. The approach used there (which is quite common)
is to simply assign random velocities according to a Maxwell distribution at the
desired temperature. There is not discrete heating phase.
-Justin
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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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