[gmx-users] How can I reconstruct the system in CGMD simulation?

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 17 17:58:22 CET 2009

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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