rasoul nasiri wrote:
yes, I know there will be limitation for modeling of Folding/Unfolding
proteins with MARtini CGFF if I want to look at complete
folding/unfolding mechanism of proteins but I want to find out localized
regions of the protein (e.g. the C- or N-termini) that they have
contribution to the denaturation mechanism.
My question is about vdwd in beads of water. Is it OK if I select
distances of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I
have to reconstruct the system in smaller vdw distance of the water
beads for doing my purpose. and Which commands of Gromacs can do it?
The values in vdwradii.dat are not used in the actual simulation. They are used
by tools like editconf and genbox when building the system. Attractive and
repulsive parameters for nonbonded interactions are defined by the force field,
which is assembled in the input to mdrun.
-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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