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mbdx6cw3 / func_gra_code

This program can be used to oxidise a pristine graphene flake to make graphene oxide, generating the input files (.gro and .itp) required to perform an MD simulation using GROMACS.
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Periodic graphene oxide #1

Open yel21 opened 9 months ago

yel21 commented 9 months ago

Dear Dr. Christopher D. Williams‬,

Thank you very much for your code. Could you please help me? I want to build periodic graphene oxides. Your code perfectly builds a non-periodic graphene oxide sheet. However, when I input my initial periodic graphene structure as an initial configuration as 'graphene.gro' and put the input.dat file, the variable “periodic = .true”. The final configuration of the graphene oxide did not have bonds that connected to the image across the periodic boundary conditions. Is it possible to use this code to build configuration and topology files in Gromacs for periodic graphene sheets that are infinite in the X and Y directions?

Best regards Victor graphene224.zip

mbdx6cw3 commented 9 months ago

Hi Victor,

Before running the code you need to adjust the box dimensions in the graphene.gro file such that they match the coordinates / underlying structure of the graphene sheet. I think what is happening at the moment is that, because you have not done this, the distance between carbon atoms at each end of the sheet that should be connected via the periodic boundary is too large, and the code does not recognise that they should be bonded.

Chris

yel21 commented 9 months ago

Dear Chris,

Thank you for your response. Initially, I avoided increasing the size of the periodic box of "graphene.gro" (I attached this file), but the following error occurred:

graphene_no_change_pbc.zip

At line 586 of file functionalise.f90 Fortran runtime error: Index '1345' of dimension 1 of array 'gra_x' above upper bound of 1344 The distance between the atoms in the zero image and the first periodic image was equal to the C-C bond size in the GAFF force field of 1.4 A. In this case, I used the parameter file that was prepared for the AMBER force field. Please, see the attached file

image

As I understand, this error is related to the number of atoms in the graphene sheet. If the periodic box is close to the graphene size, the problem in all cases gave me the same error. Then, I saw that in your test file, the size of the box was set to be larger than that of the graphene sheet; thus, I increased the size of the periodic box.

Is it possible to solve this error without significantly changing your code?

Best regards Victor

yel21 commented 6 months ago

Dear Chris,

I had the opportunity to start a simulation with periodic graphene using the CHARMM force field, but I wonder if you have any chance to build a graphene oxide topology in the AMBER force field? Could you please suggest where to find the parameters for carboxyl, epoxy, and hydroxyl groups?

Best wishes, Victor