Help with REACH forcefield and NMA

[Rakesh Ramachandran]

Hi,

Does bio3d have a module to derive the force constants from the MD simulation as in the REACH paper ?

If not what can be the possible set of functions in bio3d I can use to derive them as I understand that bio3d already has modules for variance-covariance matrix calculations ?

Moreover is it possible to apply different force constants to different set of residues say for a particular domain in a protein before building the Hessian and will this be ok to do in NMA.

Regards Rakesh

[Lars Skjærven]

Hi Rakesh, There is not such bio3d function, but you should check out the reach program. I think it can calculate the force constants based on an MD trajectory. You can certainly also do some R programming to obtain the force constants. Check out function var, cov etc.

[Rakesh Ramachandran]

Hi Lars,

Thanks for the reply. My question regarding Normal mode analysis was is it logical to use two different force fields like ANM for one domain and REACH for another domain in a single protein and then build the hessian.

Rakesh

[Barry Grant]

Depends on what your objective and actual purpose/question is Rakesh. Note that it is hard for us to answer this with the information you provide. However in ~90% of cases this probably a bad idea.