[gmx-users] how to run free energy perturbation!!!

[nanyu101 at sina.com]

Dear gmx-users,

   Now,I have a polymer and it has many helix conformations. I want to use free energy perturbation in Gromacs to figure out what the energy profile between two conformations is. I have never done free energy perturbations although I have used Gromacs for one and a half years. So would you please give me some advices in the following problems?

1. how to set up the input file(mdrun.mdp).I have know how to set up  the lambdas? But I do not know how to fix the two conformations in a single mdrun.

2. How to run these free energy perturbations? I think there are many windows in getting the free energy profile for every lambda value, but how to fix them? In the sampling process, how does Gromacs fix this problem?

Thanks a lot.

Best wishes,
nanyu
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