[gmx-users] Polymer simulation help and suggestions

[Caleb Tormey]

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?
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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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