[gmx-users] Polymer simulation help and suggestions

[Justin A. Lemkul]

Caleb Tormey wrote:
> Justin,
> Thank you for your response.  My simulation will involve around 30 
> chains of polymer along with varying amounts of different salts.  For 
> instance LiPF6, LiClO4 and larger molecules like 
> [1,3-dimethylimidazolium]PF6 and I am looking for the best way to 
> incorporate these.  I guess I am a little stumped as to the best method 
> for generating these.  Should I make separate .gro and topology files 
> for these? 

Yes.  You won't be able to add these polyatomic ions with genion.  You will have 
to insert them with genbox -ci -nmol instead, then #include the relevant .itp 
files into your .top file.

Parameterization of these compounds will not be trivial.  You should be prepared 
for significant effort to develop these parameters for the force field you've 
chosen, unless they've already been developed and validated.

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

> Regards,
> Caleb
> PS.  I haven't researched this part as much so it is possible this has 
> already been answered and I just haven't come across this. 
> 
> 
> On Sun, May 23, 2010 at 10:47 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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.
> 
>     -Justin
> 
> 
>         Thank you in advanced.
>         Regards,
>         Caleb
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================