[gmx-developers] introduce effective potential
Berk Hess
gmx3 at hotmail.com
Mon Apr 19 10:44:56 CEST 2004
>Dear All,
>
>I would like to replace the dihedral potential energy function (formed
>by 4 atoms i,j,k,l) by the effective potential
>
>U_eff(\theta_{ijkl}) = KT*q/(q-1)*log(1 + KT*(q-1)*[U(\theta_{ijkl}) +
>epsilon])
>
It seems to me that the second factor KT in this formula should be (1/KT).
>where q and epsilon are the parameters, U(\theta_{ijkl}) is the original
>potential. This effective potential is smoother (depends on value of q)
>than the
> originial
>one and therefore the sampling is enhanced.
>
>This is equivalent to introduce the scale factor:
>
>q/(1 + KT*(q-1)*[U(\theta_{ijkl}) + epsilon])
>
>into the forces which acting on the atoms i,j,k,l
>
>To this end, I have modified to code as follow (in bondfree.c)
The modification is not correct, because the shift forces for the virial
calculation are not modified and thus the pressure will be incorrect.
You should scale ddphi just before the do_dih_fup call or F* in dopdihs.
Note that you did not modify the potential value and thus your potential
energy will be incorrect.
If you want it to be correct you need to apply your conversion formula
to vpd (or V* in dopdihs).
Berk.
_________________________________________________________________
Talk with your online friends with MSN Messenger http://messenger.msn.nl/
More information about the gromacs.org_gmx-developers
mailing list