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

[James Starlight]

Justin,

yes, the main task is the parametrization of the simple 2D lattice
which I created from sp3 carbons as the nodes. Now the main task is
the reducing of that model  to simplest 2D lattice made from 1 type of
any atom connected with the 3 adjacent nodes via flexible bonds.

Might I define new atom type for that node   in the atomname2type.n2t
file placed to the work dir or should I add that atom to the ffbonded
of the opls or gromos ff ?

James

2013/1/3, Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> --
> ========================================
>
> 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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