[gmx-users] calculate potential with tabulated non-bonded interactions

[Justin A. Lemkul]

Liu, Liang wrote:
> Well my first question is: if the pdb2gmx command must take a force 
> file? I guess it should be necessary. Then the available list contains 
> amber and others, but not user-specified potential. This will affect the 
> future simulation or calculation?
> 

Yes.  Gromacs allows you provide tabulated potentials for van der Waals and 
Coulombic interactions (nonbonded), as well as bonded terms.  The complication 
is that force fields are somewhat more complex than that.  For instance, there 
are intramolecular terms (such as 1-4 interactions) that may or may not be 
scaled, depending on the force field used.

If you have a completely custom force field and you are trying to override all 
elements of an existing force field, it is better to simply write a new force 
field rather than attempt to hack an old one.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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