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On February 14, 2011 at 3:28 PM Moeed <lecielll@googlemail.com> wrote:<br />
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Dear experts,<br />
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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).<br />
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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?<br />
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<p style="margin: 0px;">How close are the polymers?</p>
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2- I have switched off electrostatics so I am using<br />
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free_energy          =   yes<br />
init_lambda          =   0 <br />
delta_lambda         =   0<br />
sc_alpha             =   0.5<br />
sc-power             =   1<br />
sc_sigma             =   0.3<br />
couple-lambda0       =   vdw<br />
couple-lambda1       =   none<br />
couple-intramol      =   no<br />
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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 +).<br />
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<p style="margin: 0px;">Have you thought of using Bennett's Acceptance Ratio? This make for a little more work but knowledge of your error is nice.</p>
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Please let me know your comments/point of view about the system and setting I am using.<br />
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Thanks<br />
Moeed<br />
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<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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