Dear lammpsers,

I'd like to compute the free energy profile of the bonded interactions in my system, but it doesn't seem to be possible in thermodynamic integration... Is there a way around this problem? I can compute the lj interactions fine, but it's the bonds that are of interest to me at the moment...

With best wishes,

Anna

Dear lammpsers,

I'd like to compute the free energy profile of the bonded interactions in my system, but it doesn't seem to be possible in thermodynamic integration... Is there a way around this problem? I can compute the lj interactions fine, but it's the bonds that are of interest to me at the moment...

this is confusing. can you reword this to explain in more specific

terms where the problem is?

axel.

Dear Axel,

Thanks for your email. I have a coarse grained polymer system with FENE bonds and LJ pair-wise repulsion (self avoiding chain). What I did is to look at the free energy profile based on thermodynamic integration, in which case I could look at the free energy profile when lj component is turned off and on, but turning off FENE bonds cannot really be turned off, and therefore I am interested whether there is a way to see the free energy contribution of the FENE bonds?

Hope this helps!

With best wishes,

Anna

Dear Axel,

Thanks for your email. I have a coarse grained polymer system with FENE bonds and LJ pair-wise repulsion (self avoiding chain). What I did is to look at the free energy profile based on thermodynamic integration, in which case I could look at the free energy profile when lj component is turned off and on, but turning off FENE bonds cannot really be turned off, and therefore I am interested whether there is a way to see the free energy contribution of the FENE bonds?

well, i suppose you would have to alter fix adapt and the fene bond

style to allow turning those off. it obviously has not been

implemented. i would assume that nobody has yet needed it or somebody

might have tried and decided it is too complex. hard to say from my

perspective. as you know, a lot of the code in LAMMPS gets implemented

and contributed by individual people because they need an additional

feature and then just go ahead and implement it.

not much of a help, but that is all i can offer.

axel.

Dear Axel,

Thanks for your quick response! I'll try to figure this out.

With best wishes,

Anna

By the way, if anyone else has any ideas on how to do this, any input is appreciated. I looked at ti/spring and ti/rs commands, but running them both causes problems- illegal fix (although the package is installed and I am using it exactly as in example in documentation) ...