The correction of the mean force to calculation of free energy in CP2K
zhe8... at gmail.com
zhe8... at gmail.com
Wed Nov 6 01:46:48 UTC 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20131105/71f7052d/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: md-constraint.zip
Type: application/zip
Size: 335833 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20131105/71f7052d/attachment.zip>
More information about the CP2K-user
mailing list