many thanks, mic<br>After youy explanation, i do understand "PMF" much better.<br>I think "PMF" may be useful for looking for the intermediate of two minimal conformations according to your explanation.<br>It is fortunately to learn "PMF" can be calculate in gromacs, then let me have a try!<br><br>Zhjim<br><br>>The potential of mean force is actually the free energy difference.<br>> between the states at the two well defined endpoints of an arbitrarily <br>> defined reaction path.<br>> This "reaction path" can be, for example, the path traveled by a molecule<br>> in a solvent through a distance dz normal to a surface. The result would be <br>> the free energy of adsorption if z(lambda_0) is a point well away from the<br>> surface and z(lambda_1) is the equilibrium distance of an adsorbed<br>> molecule. Other frequently used reaction paths are the path that<br>> an ion travels through a ion channel or the path defined by <br>> a rotation trhough a dihedral angle in a molecule in solution.<br>> <br>> The, maybe confusing, name PMF comes from the fact that the PMF is <br>> customarily calculated as the integral of the average force as a function <br>> of lambda going from lambda=0 to lambda=1, which in the above case would<br>> correspond to the two states defined by the molecule-surface distance<br>> z(lambda_0) and z(lambda_1)<br>> If you write the average force as <F> = <dU/dz>, put that expression<br>> in the integral and replace z by lambda you see that this is nothing elso <br>> but a special case of a thermodynamic integration ... see, for example <br>> textbooks such as Allen, Tildeslay for more detailed explanations.<br>> <br>> You can calculate the PMF in gromacs with the pull code. Be careful<br>> though, in all but the newset version of Gromacs there seem to be a couple<br>> of bugs in the pull code.<br>> <br>> mic<br>> <br>> <br>> __________________________________________________<br>> Do You Yahoo!?<br>> Tired of spam? Yahoo! Mail has the best spam protection around <br>> http://mail.yahoo.com <br>> _______________________________________________<br>> gmx-users mailing list<br>> gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> <br><font style='font-size:14.8px'> </font>
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