[gmx-users] free energy-couple-intramol options

Moeed lecielll at googlemail.com
Mon Feb 21 19:28:22 CET 2011


I read through the couple-intramol options (yes and no) good many times but
I can not still realize what is the difference and which option I should
select. I am having a hydrocarbon system (polyethylene in hexane as
solvent). Can anyone help me understand these options please? (in plain
english) option yes, says something about FF of large molecules which is my
case...but I dont see the statement: nb interactions might lead to
kinetically trapped vaccum conformations?!

Also, as with the electrostatics treatment in my hydrocarbon system I am
still unsure if I need to include electrostatics potentials. I digged into
the literature and found the following articles containing nonpolar polymers
where vdw is the only nonbonded term in the FF.



Please let me know your comments

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