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

[Anton Feenstra]

nanyu101 at sina.com wrote:

> 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. 
[...]

It depends a lot on the behaviour of your system how you would want to do this.
If the dynamics of your polymer are fast enough and you can get long enough
simulations, you might get to finding a 'true' equilibrium in your simulation
that encompasses both states you are interested in. IN that case, you can simply
count the amount of time spent in each state.

Otherwise, you would have to simulate one state and 'integrate' it towards the
other. In principle this is very hard to do. There are (hopefully) other people
on the list who can (should) explain this better...! ;-)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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