towhee-users Mailing List for MCCCS Towhee

Hi All,

I'm trying to set up a bulk benzene simulation. I want to use completely rigid 12-site benzene model. I pulled most of the lines for a new "benzene2_ff" force field file from Charm27 ff file. Then I modified the lines, setting specific rigid bonds and angles. When I tried to skip the torsion energy parameters, setting the number of torsion types to 0, the Towhee complained, demanding to know parameters for 4-atom graphs ( CCCC, CCCH, HCCH). To make a test run, I had to resort to torsion type 8.  I was wondering if this is a good way to set up my simulation or if I might be able to skip the torsion set up at all.
The problem with setting torsion type to 8 is this. When I let Towhee (ver. 6.2.2) to initialize my molecules on the simple cubic grid, molecules are not planar. It is only when I give the explicit atomic coordinates that I get the planar molecule. 
I attach the force field file (benzene2_ff) along with the towhee input file (towhee_input).

Thank you,

Anatoli Milischuk
Department of Chemistry
Colorado State University


      

Dear Towhee-Users:

I am just learning Towhee and want to put molecules/atoms in carbon
nanotubes by Configurational-Bias Monte Carlo.  I am trying to learn the
commands accepted in the towhee_input script.  Basically, the
'Walt2001_Nanotube' example is perfect except for I only want the water to
be inside the carbon nanotube, not outside.  What do you suggest I do?

Is it possible to artificially weight all positions outside the CNT to
suffer a high potential energy penalty?  While that seems like a somewhat
inelegant solution, I'd rather simply restrict the box to inside the carbon
nanotube, but I do not know how to make a box that isn't orthorhombic.
Thank you for any insight.

-- 
Prashant
prk17/Yoshis88

Hello all:

  I want to use CBMC method to generate several polymer structures of
amorphous state and then use these structures as the initial structures for
MD calculations.

  Firstly, I aimed at generating structures of one linear polymer chain. I
used single box with NVT ensemble to generate a polyethylene chain, which is
consisted of 100 monomers, at 1.0g/ml density based on Gromos FF. 
 I read the Towhee Manual and feel setting pmpivot to a large probability
may help me obtaining good results. The MC simulation does work and output a
sequence structures. By checking these structures, I found there is not much
globally change between these structures (i.e. the backbone of polymer looks
very rigid).
  Does someone can give me some suggestions of how to set the options in the
input file to generate amorphous polymer structures? 

  Secondly, I also want to generate structures of several linear polymer
chains in one system. The MC simulation was performed with the input
settings same with the above one chain case. However, the output file gave
the message that the intermolecular overlapped. I think such error may be
due to the options setting for the growth process but I have no idea of how
to correctly set these options. I will be appreciated for any suggestion
relating the way of avoiding the error.

 Best regards

 Caoch
 Tokyo Institute of Tech