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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