[gmx-users] Re: Simulation of 2D lattice model

Justin Lemkul jalemkul at vt.edu
Wed Jan 2 11:52:20 CET 2013

On 1/2/13 4:36 AM, James Starlight wrote:
> Justin,
> I've already tried use g_x2top for the model of the system built from
> regularly spaced C-atoms ( with included hydrogens to specify sp3
> hybridization).
> By means of that command I've created topology for my lattice with big
> force constant ( for the simulation of the very rigid structure)
> g_x2top -f lattice_h.pdb -o lattice.top -ff oplsaa -kb 500000 -kt 4000
> -kp 500 -remdih
> the main problem which I've forced is the  the absence of
> automate-generated impropers. As the result my lattice model at the
> beginning of the simulation (langevin's dynamics, nvt) have been
> perturbed and simulation finished with alot of lincs warnings. How I
> oculd fix it ? Should I use another atom names in the initial model (
> e.g from polar hydrogens )?

A bunch of sp3 carbons with attached hydrogens will not have any impropers, 
because the carbon centers are not planar.  Atom names are irrelevant; g_x2top 
will do what you tell it based on bonded geometry.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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