Dear Sir/Madam,
I read from the literature that implicit solvent models convergent faster,
just it may reach equilbrium faster than explicit solvent. Thus, I am
writing to ask what is the typical stimulation time for a system with 700
residues using implicit solvent (GB) in Amber?
I noted that the potential energy remain more or less constant after 200 ps,
then, I run the production period for a further 1 ns. Is it an acceptable
time for implicit solvent (GB) calculations? if not, how long should be used
for publication purposes?
Best regards,
Catherine.
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Received on Wed Feb 14 2007 - 06:07:48 PST
