Molecule command: 98 atom molecule not loading ERROR

LAMMPS LAMMPS Beginners
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To whom could lend me some help,

A a beginner I am first creating the simulation box as a multi-component system. I downloaded the Force-Fields from the ATb server, for which I have successfully simulated several MD and BD runs. The procedure I have followed is:

  1. Generate LAMMPS input scripts using Moltemplate and compiling the “.lt” files extracted from ATb for the FF and the molecule topology.
  2. From the generated “data” file I manually produce the molecule “.txt” file to be compiled along with the “system.in.init” and “system.in.settings” files.
  3. I follow up the commands that I provide in the “run.in” file here.

I have successfully loaded the molecule I name as “trans-OMCA.txt” that has 22 atoms. However, when trying the same for the “PGAC.txt” molecule that holds 98 atoms, I get the following error:

ERROR: on proc 0: Unexpected line in molecule file while looking for the next section: 98 20

I have double checked that the “PGAC.txt” follows the same pattern as the “t-OMCA.txt” molecule succesfully compiled. I have already tried the following, but nothing works, but one try gave me a hint on what the problem is:

  • Fix the topology data amounts while doing “create_box” so that this includes what is necessary for this “PGAC.txt” molecule, but any # seems to work.
  • I wondered if the 98 atoms could be too much for the molecule command to be able to compile, thus I tried to fix 97 atoms instead of 98, and commented the Coords, Types, and Charges; for the leftover molecule #98, and the molecule command strangely compiled this modified “PGAC.txt” file, but without placing the Types for each atom. This results in not being able to used the tagged molecule to be inserted in the simulation box with the “create_atoms” command with which I previously inserted the “t-OMCA” molecules successfully.

The latter test I performed gave me the hint on the possibility that 98 toms may be too much for a molecule to hold. Thus, my fina try was to use a similar molecule, but with 62 atoms (CTAB.txt) to see if the amount of atoms is really affecting, or if there was something I was missing. The result was that this “CTAB.txt” molecule was compiled correctly. Being quite similar to the “PGAC.txt”, but with 62 atoms instead of 98, made me notice that I am not missing anything in terms if the necessary topology data included

However, I would really like to know if there is something I can do to insert replicas of this “PGAC.txt” molecule within my simulating system, given that this “molecule” command is limiting the atom count, and this “CTAB.txt” is not enough for my purposes.

Regards
jfernando

P.S. I tried to upload the files I mentioned before, but it seem that is not a feature available for new users. In case there is a reply from someone who requests the files as usual, and somehow the system enables me to upload them for not being a new user anymore, I will certainly do it.

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This makes no sense and there is no such limit.

What is much more likely is that you have a mismatch between the number of atoms and the number of entries in one of the sections.

You should be able to upload files now. Please also have a careful look at the guidelines posted here and provide the information requested like LAMMPS version and platform.

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Thanks akohlmey

You were right. The dummy mismatch was an extra line in the “Types” of the molecule file, and that was why the last atom was identified as an extra atom not considered in the header section. This resulted in the error previously quoted, because the labeled “98” atom was taken as a “#99” atom.

Now this works fine, but following to perform energy minimization SD, and then MDs with thermostat (NVT) in 3 different computing systems and installation, I have few doubts that are completely different to the initial question and topic. Should I start a new question with different topic name?

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Yes