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

[James Starlight]

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 )?


James

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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>