[gmx-users] bond conversion between charmm and g96

[라지브간디]

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Dear Justin,


Thank for your pointing out my issues. I just want to know how it can be converted.


I have referred the equation in chapter 4 and do not know exactly how I use them. 


For example, The C-O bond distance and force constant written as (0.112  and 3.7000e+07 ) in gromos, whereas  in charmm27 written as ( 0.1128 and 933032.0). 


I found the equation for g96 type covalent potential Vb (rij) and force constant Fi(rij) and don't know how do i use this for above purpose? 


Could you elaborate an example how it can be done? Thanks a lot.







> Thanks for the mail justin. 
> 
> 
> In charmm27.ff, the value for bonded are in b0 and ko format, whereas the 
> gromos uses them in different way? If so, how do i convert between them? 
> 
> 
Please consult the manual, Chapters 4 and 5 for all the relevant equations 
and implementation. 


> 
> The value i incorporated for specific atoms are from published journals. 
> Thanks in advance. 
> 
> 
I think you're missing my point though. Just because something is 
published, doesn't mean you can use it for whatever purpose you like. 
People spend years working out properly balanced force fields, and if you 
try to put in some new atom type, it upsets the balance of every 
interaction. You may be OK within the context of CHARMM (depending on what 
the paper is, and what parameter set they modified), but I can guarantee 
you that if you're trying to incorporate CHARMM parameters into GROMOS, all 
you're doing is producing a pile of trash. You can probably "make it work" 
from a topology standpoint, but you shouldn't be doing it. I hope my 
perspective is clear; I'm trying to save you from wasted effort.