[gmx-users] Polymer simulation help and suggestions

Caleb Tormey ctormey at mymail.mines.edu
Sun May 23 18:39:46 CEST 2010

Hello all,
I have just started working with GROMACS and simulation in general.  I will
be doing simulation of PEO with various ions and need a little help.  I have
read a great deal of the documentation and now edited the appropriate .rtp
and.itp files to generate my polymer from a .pdb file using pdb2gmx and it
seems to be generating my topology and .gro files correctly.

My question is if I wish to keep a static bond length do I address this in
the bond information or is there something in the .mdp file that will
address this?

I also would like some suggestions for a few other things.  To make my
preliminary polymer I used a molecular modeling/editor program called
Avogadro but was wondering if there is something better to use to create the
random walk long chain polymer?

Also, I was just going to create my own ion files and use genion to
incorporate those into the simulation but didn't know if this was the best
way to do this.

And lastly when I need to create a multiple polymer simulation my plan was
to use genconf and generate a crystal with the appropriate number of
polymers and then just heat it up to melt it.  This seems to be a good way
to do it however, another person in my group who used NAMD used a program
called PackMol and had some success and was wondering if anyone else had
used this program and would recommend this route?

Thank you in advanced.
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