[gmx-users] Position restraints and free energy calculations

[Kortzak, Daniel]

>Wouldn't just using the pull code to do umbrella sampling be a much more
>straightforward approach?  You don't have to deal with compensating for
>artifacts associated with the restraint potential during decoupling and removing
>a charge from the system.
>
>-Justin

Hi Justin,

thanks for your fast reply. So far I did not consider this because on alchemistry.org they say beginners should start with the decoupling approach and all the papers I read so far also do only the decoupling approach (even in the simple case of a single ion binding to a protein). But of course this is no reason why I should not try the pulling. One real problem might be that the binding site is buried relatively deep in the protein. First I have to read a little more but soon I will be back with questions regarding the pulling method :)
Nevertheless I am still wondering about the other questions I asked (just curiosity, maybe I at some point this will be important for me).

Daniel


------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------