[gmx-users] free energy

Moeed lecielll at googlemail.com
Tue Feb 15 00:28:41 CET 2011

Dear experts,

I am going to do solvation FE of polymer (polyethylene) in a hydrocarbon
solvent. I have prepared a system consisting of 4 polymer chains and 480
hexane molecules with the actual density of polymer solution (~ 0.5 g/cm3).

1- For such a study I dont know how many polymers I need to have in my
system. If FE can be done with only one chain, am I making system bigger in
vain? Does this matter affect the accuracy of results?

2- I have switched off electrostatics so I am using

free_energy          =   yes
init_lambda          =   0
delta_lambda         =   0
sc_alpha             =   0.5
sc-power             =   1
sc_sigma             =   0.3
couple-lambda0       =   vdw
couple-lambda1       =   none
couple-intramol      =   no

In David Mobley's turorial the last three lines are not included. I wanted
to know if I am to run say 10 simulations for different lambda, what purpose
does the last three lines serve in 4.0.7  ? I got very close values in that
tutorial without these settings. ( I know what these lines mean, just
curious how these three lines affect the results in 4 X +).

Please let me know your comments/point of view about the system and setting
I am using.

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