I am trying to perform a simulation with a graphite structure in the middle of the box (5 stacked graphene layers), something like a membrane. To make the graphite infinite in the x-axis in using the “periodic-molecules = yes” option in the mdp file. However, when I run the minimization energy step seen that the graphene layers are not coupling with their periodic images in the x-axis.
To ensure that the layers are coupling to each other I just have to guarantee that the PBC atoms are within the “bond” distance of the atoms from the original box? Or there is something that I should add to the ITP file? Does anyone have any tips or advice?
I am attaching a picture of the layers with the PBC before and after the minimization.
“periodic-molecule = yes” in .mdp file does not generate bond potential automatically between the image, you have to manually including them in the topology file
As Alessandra said, I have tried this, with help from this forum. I created an infinite (linear) DNA that was one base pair longer than I wanted on each side (top and bottom). I then (manually, eventually I will script this) went in and changed all references (bonds, angles, etc.) to the bases that were outside of my PBC box to their periodic equivalent. For a very simple example, if you wanted a 10 atom linear molecule, you would create a 12 atom molecule, cut off atoms 1 and 12 and any references, for instance, of a bond between atoms 11 and 12, you would change to a bond between 11 and 2. From what I understand, the “periodic-molecule=yes” simply alters the way some of the periodic boundary conditions are assessed to deal with molecules that are connected across the boundary.
Thank you for your explanation here. May I please follow with this discussion since I am currently having the similar system simulation using MARTINI FF for Polymer sheet.
Following your and Alessandra’s advise, if you build 12 atom molecule. And connect 11 and 2, will your 12 atom will be free atom and flowing around in the system since there is no bond connect between 11 and 12?
Also do you need to connect 11 and 2 in angle and dihedral? Looking forward to hearing from you. Thanks.
After you connect your 11th residue to your 2nd residue, you should delete the 1st and 12th residues and all references to them. The only reason I am including them is so that I can use them as reference to the connections that need to be made. It is also important to point out that the 12th residue should be the same as the 2nd residue and the 1st residue should be the same as the 11th so that all of the bonds, angles, and dihedrals are correct. And, yes, if there are angle or dihedral connections between your 11th and 12th residues (or, equivalently, your 1st and 2nd residues), then you should include those same connections between your 11th and 2nd residues.
Thanks so much for your email kind reply with such helpful information. I am currently trying this system as you suggested. However, it may because my system was built at CG scale? Or maybe because the structure is polymer sheet? When I run the simulation of polymer sheet within water, the CG water molecules just formed as ice with no movement, and even I tried with antifreeze water model. Not sure if you have observed any of these happened in your system?
