Questions Related to Mapping for Charge Transport

[Jia-Qi Gao]

Dear all,

I am a beginner user of VOTCA-XTP and am currently working with VOTCA version 2022. I would like to ask several questions regarding the mapping procedure, particularly the setup of the XML file.

My folder structure is shown in the attached files. The goal of my calculation is to map polymer chains (annealing_whole.gro) onto a DFT-calculated monomer structure (monomer_opt.xyz).

However, I encountered several issues during the mapping process.

To neutralize the monomer for the DFT calculation, I added capping hydrogens (atoms 7 and 10). As a result, the monomer_opt.xyz structure always contains more atoms than the corresponding residues in the polymer chain.

During testing, I found that the numbers of entries in the <mdatoms>, <qmatoms>, and <weights> tags must be identical; otherwise, VOTCA reports an inconsistency error.

Eventually, I prepared an XML file (system.xml) that can be processed without errors. However, the mapping still appears to be incorrect. After generating extract.trajectory_md.pdb and extract.trajectory_qm.pdb using the command:

ctp_dump -f state.sql -e trajectory2pdb

I found that the two structures are not consistent.

The extract.trajectory_md.pdb file appears as expected and matches the input structure (annealing_whole.gro). However, the extract.trajectory_qm.pdb structure seems incorrect: although the capping hydrogens are present, several other hydrogens are missing, as marked in the attached figure.

Therefore, I would like to ask whether anyone could kindly advise me on how to properly set up the XML file for charge transport calculations in this situation.

Thank you very much for your time and assistance.

Best regards,
Jia-Qi Gao