[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 
> 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? 

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.
> Regards,
> Caleb


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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