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. In other words I'd like to learn how to make
reasonable conclusions about valibility of amd simulation from the log
data. For instance 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. Below you can see fragment of amd.log according
to its last column (dUdihe) dihedral boost during my simulation was only
around 10Kcal/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.
5000 5000 -125724.393819389981 3349.271725052036
0.875240713824 0.638844371595 65.730843126304
16.528734887827
5000 10000 -125908.271357561578 3368.108560306020
0.842137000064 0.745888797627 109.297390838183
7.058739945562
5000 15000 -125863.977305051987 3378.433303408325
0.849306445405 0.816372786795 98.772000192028
3.377173759015
5000 20000 -125664.100661920500 3361.184529500082
0.885453140856 0.703613189561 54.781255272262
10.155903950865
5000 25000 -125747.326542982948 3376.096760118380
0.869773063644 0.799572446410 72.060996728851
4.105672833054
5000 30000 -125780.548153562588 3366.434282334521
0.864289106859 0.735323701847 78.745542049357
7.763776884863
5000 35000 -125730.578018928994 3369.580708143301
0.873020486280 0.755367667748 68.261416205860
6.462778693300
5000 40000 -125736.756359334220 3353.239631806500
0.872775423872 0.659386964086 68.544064849710
14.268158072671
Thanks for suggestions,
James
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Received on Wed Jul 23 2014 - 02:30:02 PDT
