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

[James Starlight]

Justin,

so why my simulation of the sp3 lattice have been crashed with the
links warnings ( which always tells about wrong geometry in topology)?

also I've tried to paraetrize completely planar (sp2) lattice but
obtain errors like that

Can not find forcefield for atom C27-22 with 2 bonds
Can not find forcefield for atom C28-23 with 3 bonds
Can not find forcefield for atom C4-24 with 3 bonds
Can not find forcefield for atom C15-25 with 3 bonds
Can not find forcefield for atom C1-26 with 3 bonds
Can not find forcefield for atom C39-27 with 3 bonds
Can not find forcefield for atom C41-28 with 3 bonds
Can not find forcefield for atom C30-29 with 3 bonds
Can not find forcefield for atom C2-30 with 2 bonds
Can not find forcefield for atom C5-31 with 2 bonds
Can not find forcefield for atom C8-32 with 3 bonds
Can not find forcefield for atom H22-33 with 0 bonds

So I've decided that the atom names is also relevant besides the
geometry which was correct in that case.


James

2013/1/2, Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> --
> ========================================
>
> 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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