[gmx-users] free energy
lecielll at googlemail.com
Tue Feb 15 00:28:41 CET 2011
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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