[gmx-users] Polymer simulation help and suggestions
Justin A. Lemkul
jalemkul at vt.edu
Sun May 23 18:47:00 CEST 2010
Caleb Tormey wrote:
> 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
> 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?
Use the "constraints" keyword in your .mdp file. See the manual.
> 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?
There are several programs that can build molecules, like xLeap (part of
AmberTools) and even VMD has some capabilities for building molecules. I don't
know about polymers specifically.
> 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.
To what files are you referring? Are you introducing new parameters of some
sort? Be aware that pre-defined ion parameters are included as part of all the
force field parameter sets packaged with Gromacs, so any new parameters must be
validated before being used.
> 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?
Either way should work fine. PackMol does a good job of generating initial
configurations given geometrical constraints, but your procedure should work if
you do sufficient heating to change the initial structure.
> Thank you in advanced.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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