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 <jalem...@vt.edu
<mailto:jalem...@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
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