AMBER Archive (2007)

Subject: AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Feb 13 2007 - 22:18:23 CST

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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