Andrei Neamtu wrote:
Hi,
I am trying to build a hydrogel polymeric system and I want to make
use of the option periodic_molecules.
In this regard I am a little bit confused..... are there any other
keywords except the option 'peridic molecules' that I have to set to
define a periodic polymer chain e.g. in the molecular topology file?
Because in the case I define a bond between the last atom of the
chain and the first one, how does the grompp and mdrun know that the
molecule is periodic and not cyclic?
As you observe, the *topology* is the same in both cases. The coordinate
file supplied in a well-formed example of each case will differ. The
.mdp file option merely changes the implementation of PBC during the
setup and/or simulation. (See manual 7.3.9) As an exercise for the
reader, presumably you could construct a coordinate file with a cyclic
version of the same topology, and observe that with and without
"periodic_molecules" you'd get the same simulation slower and faster,
respectively.
I also suppose that the angle and dihedrals that cross the periodic
border should also be defined.
Yes, in the same manner as normal versions of such interactions.
Is there a place where I can find how to define periodic molecules in Gromacs?
There are some tidbits here
http://oldwiki.gromacs.org/index.php/Carbon_Nanotube, some of which
pre-date the use of "periodic_molecules" I think.
If any of this is bewildering, then doing some tutorials of simpler
GROMACS simulations might be a good idea, to get an idea of the workflow :-)
Mark
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