[gmx-users] Potential of mean force

[Mark Abraham]

On 25/05/11, 郭漫  <pysgm2010 at hotmail.com> wrote:
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> Hello users,
> I followed the tutorial steps to do umbrella sampling of GROMACS Tutorial, (This is the tutorial site http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html) and get the
>  PMF is close to -50 kcal/mol. However, when I put amber99sb parameter 
> instead of gromos96 53a6 parameter, without changing the other parameters and steps，the result is about -35 kcal/mol. I 
> don't know why the difference  is so large between them, and i need your help for explaining what is the reason for the difference, simply because I changed the force filed, or some other possible causes.
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If all you've changed is the force field, and these simulations are long enough to produce converged measurements, then "welcome to the jungle". Different force fields have been demonstrated to be good or bad on different types of systems for different types of properties. Choosing the right force field is normally a most important and sometimes the most time-consuming part of doing simulations properly. Read widely, and take good notes.

Mark
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