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

[Justin Lemkul]

On 1/2/13 7:15 AM, James Starlight wrote:
> Justin,
>
> so why my simulation of the sp3 lattice have been crashed with the
> links warnings ( which always tells about wrong geometry in topology)?
>

Incorrect geometry is not the only cause of LINCS warnings.  I haven't seen 
nearly enough information to know what the cause of the problem is.

> 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.
>

No, the names don't matter.  The program is simply telling you that you have 
some atoms that don't fit within the criteria of existing .n2t entries.  You may 
have to write your own in order for the program to complete successfully.  The 
H22 atom is particularly instructive - it says zero bonds, which means that it 
is not within the distance cutoff to be actually bonded to anything.

-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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