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

[James Starlight]

Justin,

 I want to simulate lattice with flexible nodes ( to examine
fluctuations of that system by mens of Normal Mode Analysis). If I
choose sp3 carbons as the nodes I obtain such lattice. But In that
system hydrogens are also present which are not desirable in my system
( i want system consisted of only one type of atoms). On contrary if I
choose sp2 hydrogens as the nodes I obtain completely rigid lattice
which are not suitable for me.

I suppose that united-atom model could be suitable for such flexible
lattice but I've failed to apply g_x2top  on my lattice with gromos
force field ( I have no problems with the opls-aa for this system).

Here I've obtain errors like

Can not find forcefield for atom C116-70 with 3 bonds
Can not find forcefield for atom C119-71 with 3 bonds
Can not find forcefield for atom C120-72 with 3 bonds
Can not find forcefield for atom C121-73 with 3 bonds
Can not find forcefield for atom C122-74 with 3 bonds
Can not find forcefield for atom C124-75 with 3 bonds
Can not find forcefield for atom C125-76 with 3 bonds
Can not find forcefield for atom C126-77 with 3 bonds
Can not find forcefield for atom C127-78 with 3 bonds
Can not find forcefield for atom H01-79 with 0 bonds
Can not find forcefield for atom H02-80 with 0 bonds
Can not find forcefield for atom H03-81 with 0 bonds
Can not find forcefield for atom H04-82 with 0 bonds
Can not find forcefield for atom H05-83 with 0 bonds

So it seems that the bonds  between C and H atoms were not recognized
correclty in case of gromos-ff. Must the some corrections be done in
the atomname2type.n2t file ?


James

2013/1/2, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 1/2/13 3:08 PM, James Starlight wrote:
>> Justin,
>>
>> I want to simulate flexible lattice consist of only one type of atoms
>> (nodes). So the planar (sp2 ) carbons are rigid. On other hand more
>> flexible (sp3) carbons  connected with hydrogens but I want that
>> hydrogens were not included in my lattice. Should I use another
>> (what? )atom-type for the node of my lattice ?
>>
>
> I'm sorry to say I don't understand what you're saying.  If you want a
> lattice
> of carbon atoms, you can surely develop a united-atom model of such a
> lattice
> and never involve hydrogen atoms of any sort.  Again, valence depends
> entirely
> upon what you define in the topology or its precursors (.n2t or .rtp).
>
> -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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