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
--
========================================
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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