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

James Starlight jmsstarlight at gmail.com
Wed Jan 2 10:36:48 CET 2013


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

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 )?


2013/1/1, Justin Lemkul <jalemkul at vt.edu>:
> On 1/1/13 2:01 PM, James Starlight wrote:
>> Have someone else any ideas how the topology for a simple 2D lattice
>> could be done ?:)
>> I've tried to build it manually but for the system of 48 nodes
>> definition of the angles and impropers have appeared very routinely :(
> For regularly spaced atoms, g_x2top should do it.
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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