[gmx-users] Polymer simulation help and suggestions

Caleb Tormey ctormey at mymail.mines.edu
Mon May 24 00:08:58 CEST 2010

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?
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> 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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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