meisam valizadeh kiamahalleh wrote:
Dear Justin
Thank you very much for your prompt reply. I have read about your Perl
scripts. Kindly, would you please let me know where did you exactly set
that Lambda must increase from 0 to 1 by increment of 0.05? which
parameter in your energy stuff stating that Lambda must increase by 0.05
in every step?
I do not make use of methods where lambda changes with the time step. There are
significant known artifacts of doing so. All the relevant .mdp options are
explained in the tutorial, specifically:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
Please see the "Notes on .mdp settings" section, particularly the init_lambda
and foreign_lambda settings.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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