GROMACS version: 2020.2
GROMACS modification: No
I am simulating the deposition of C60 molecules onto a graphene sheet. I am inserting the C60 molecules using gmx-insert. I am trying to insert the molecules in a layers instead of random insertion. So, I provided a position .dat file with the initial coordinate and used -dr option to randomize the x and y coordinate all over the box and allowed for 1nm displacement in the z direction. I am inserting 4000 molecule. Sometimes I need to insert the molecule in a certain position with respect to the previous inserted molecule position (for example the same x and y for the last molecule but different z). I failed to do that, because each molecule is inserted with respect to the position .dat file with the allowed displacement and hence, complete layers are formed along the x-y plane instead of depositing the molecules above each other along the z direction. What I thought might be a solution is to insert the molecules with respect to the previous molecules position.
What I want to do is similar to the attached image (picture number 2) (at some positions, you might have molecules up to 3nm in z direction before a complete layer along the x-y plane is formed. I failed to do that using the randomize option -dr because every time, it will randomize the x and y as long as it is possible instead of inserting the molecules vertically (in the z direction).
I have attached what I have achieved in my trial (picture 1), showing how the molecules are inserted along the x-y plane before the z, and what I want to achieve (picture 2) where molecules were able to be inserted in the z direction before completing the x-y layer.
Is it possible to extract the coordinates for the center of mass of the last inserted molecule (so that I can write it in my .dat file and use it as a reference for the next molecule insertion) ?
is it possible to insert the molecule in a position with respect to the last inserted molecule ?
If both options are not possible, is there any suggestion on how can I do that ?
Picture number 2 is from the paper: Morphology of a Bulk Heterojunction Photovoltaic Cell with Low Donor Concentration
By: Thomas Lee, Audrey Sanzogni, Ningxin Zhangzhou, Paul L. Burn and Alan E. Mark
Please let me know if anything is unclear.