GROMACS version: 2023.3
GROMACS modification: Yes
Hi all! This may be a very basic question and apologies if so, but if I am building a decanoic acid membrane with packmol (using decanoic acid generated with molefacture), would I only need the topology file for a single decanoic acid, or for the whole system? I’m able to generate a packmol system using C10 (both with pdb files converted with obabel, and with ones I generated with vmd) but I keep getting a bit confused with the topology and steps to ensure I can actually run the simulation. Thank you so much!
Hello,
You just need one topology (.itp) file per molecule type. So if you have in your system two molecule types, lets say decanol and water, you will need a .itp file for water and one for decanol. These (together with your force field files) contain the information needed to compute the forces and run the simulations.
What depends on the number of molecules is the topology of the systems, that is, the .top file. If you have, say, 500 decanol molecules and 10000 water molecules in your system, than your topology of the system must include in order the topology of these molecules and their number, something like:
#include “ff stuff”
#include “decanol.itp”
#include “water.itp”
[ molecules ]
decanol 500
water 10000
The change of the number of molecules in your box (as long as you don’t change their order, e.g., you put water molecules before decanol ones in your .gro/.pdb files) is reflected only in the [ molecules ] section of your system topology, as all these molecules are identical and as such are all described by the same .itp file.
Oh my gosh, thank you SO much @obZehn- this is the perfect clear explanation for what I’ve been struggling to find. I will give this a shot, thank you so much!
No worries, glad I helped!
Also, I don’t know what force field you are using, but you may want to build a bilayer in CHARMM-GUI. I don’t know if you are using CHARMM36 force field, and anyway I am not sure they have decanoid acid as an available molecule in the lipid repository, but you can build a simple bilayer in CHARMM-GUI webserver and look at the output you get for GROMACS simulations (e.g. .top file and ordering of various sections there and in the .gro/.db files). You can learn a lot by just cross comparing what is a proper output and what you are getting wrong now in your files.
Thank you!! That’s a great suggestion to compare the output from the typical bilayer builder. I’ve used it lots for C12-16 membranes but unfortunately it doesn’t contain C10 which is what I want to use :( but that sounds like a great suggestion for how to still use it as a guide, thank you!
Hi
I have a doubt regarding the all-atom decanoic acid simulation. I have generated the decanoic acid bilayer using packmol. Currently, I am stuck with generating the .itp file. Could you please tell me about the procedure through which you obtained the decanoic .itp file?
Thanks in advance