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

[Justin Lemkul]

On 1/3/13 2:46 AM, James Starlight wrote:
> 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.
>

OK, so all the talk of a 2D lattice and issues assigning impropers really wasn't 
what you wanted after all?  This whole thread has gotten to be very meandering 
and contradictory, I'm sorry to say.  Only now after several days of posts do 
your real goals come out.

> 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 ?
>

There are no explicit hydrogens in any of the Gromos force fields for atoms like 
these (hence "united atom"), and IIRC there are no .n2t files for any of them. 
So it's not a matter of changing an .n2t file, it's a matter of creating one.

-Justin

-- 
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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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