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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