[gmx-users] free energy

Michael Shirts michael.shirts at virginia.edu
Tue Feb 15 20:06:33 CET 2011

One other thing I would point out is that the solvation free energy is
dependent on concentration.  you will get a different result with 4
polymer chains vs 3 vs 3, etc.  Make sure you understand the
dependence.  Also, the free energy will depend on the polymer chain

Polymer and finite concentration calculations are harder to interpret
than monomer and infinite dilution calculations.  Make sure you
understand the differences.   I'm not sure understand all of them,
though, so you'll have to think about it yourself!  Basically, you
need to make sure the physical picture of the molecules in gromacs is
the physical picture of the realistic molecular system itself.

On Mon, Feb 14, 2011 at 6:28 PM, Moeed <lecielll at googlemail.com> wrote:
> 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.
> Thanks
> Moeed
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