The correction of the mean force to calculation of free energy in CP2K

zhe8... at gmail.com zhe8... at gmail.com
Wed Nov 6 02:46:48 CET 2013


Dear YE-FEI LI
      I'm a rookie of cp2k, i run a cp2k constraint dynamics download from 
this forum, but i don't understand the output. Have you ever done some 
works about free energy calculation before? My question is that:(1)output 
about colvar in "MD-COLVAR.metadynLog" is from5to6,but we set the value is 
from3to4 in input file,they are different.(2) the output"MD-1.ener" is the 
potential energy,right? and how can i get the free energy, i don't see the 
option in free _energy print.

thanks a lot

zhe

在 2013年10月1日星期二UTC+8上午6时20分22秒,YE-FEI LI写道:
>
> Dear CP2K users and developers:
>     I am interested into calculation of free energy under a designed 
> reaction pathway, and I have some puzzle about the basic idea for 
> calculating the free energy by utilizing thermodynamic integration and 
> Lagrangian multiplier. The mean force can be obtained from Lagrangian 
> multiplier plus some specific correction according to different constrain. 
> For one bond length constrain, the mean force is the average of Lagrangian 
> multiplier. However, for other constrain, the mean force might not be the 
> average of Lagrangian multiplier, and the correction is needed.
>     For instance, if I use the distance difference of r12-r34 as 
> constrain, it seems the mean force is still the average of Lagrangian 
> multiplier. (Am I correct?) However, if I use distance difference of 
> r12-r31 as constrain, it seems the correction is needed, because r12 and 
> r31 is coupled. (Am I correct?) In this case, if I want to calculate the 
> free energy along r12-r31, CP2K will not do the correction automatically, 
> since CP2K only output the Lagrangian multiplier. Thus I must do the 
> correction by myself by using the trajectory of MD? 
> Best,
> Yefei
>
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