From: James Starlight (jmsstarlight_at_gmail.com)
Date: Wed Jul 23 2014 - 06:30:12 CDT
Dear Amber users!
In this topic I would like to talk about information obtained from the
amd.log concerning the reasonability of the values of boost potentials
applied to my system. For my case I'm simulating protein in explicit water
with the task to refine its loops appling position restraints on part of
the protein (which I'd like to keep unchanged). Firstly I've performed cMD
with no restraints to obtain all values needed to compute boost and alpha
according to the impirical formuli presented in manual. Then I run 2 boost
aMD with applied of the position restraints on the bigger part of the
protein and see amd.log. According to themd.log the value of dihedral
boost added to my system per step during amd simulation has been ~ 10
Kcal/mol on each step. I wounder if the dihe boost of this value have been
applied to the whole protein (including its restrained parts) or only to
its unrestrained (in my case loops) parts? What the reasonable dUdihe
should be expected in principle for the simulation of protein consisted of
~ 300 amino acids? I guess that this value should be nuch biger than
several Kcal/ mol to obtain better sampling.
Thanks for suggestions,
James
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