Clarification on XML input format for GaMD-OpenMM (gamdSimulation.py)

[ttpatel100]

Hello,

I am trying to run an RNA GaMD simulation using this repository, but I’m running into issues with the XML input. My current XML looks like this:

<System>
    <InputFiles>
        <PDB>PDB_FILENAME</PDB>
        <ForceField>amber14/protein.ff14SB.xml</ForceField>
        <ForceField>amber14/DNA.bsc1.xml</ForceField>
        <ForceField>amber14/RNA.OL3.xml</ForceField>
        <ForceField>amber14/tip3p_standard.xml</ForceField>
    </InputFiles>
    <NonbondedMethod>PME</NonbondedMethod>
    <NonbondedCutoff>1.0</NonbondedCutoff>
    <Constraints>HBonds</Constraints>
</System>

When I try to run the simulation with run_gamd_interactive.py, I get warnings like:

Warning: parameter in XML not found in config. Spelling error? InputFiles
Warning: parameter in XML not found in config. Spelling error? ForceField
...
Exception: No valid input files found. OpenMM simulation not made.

It looks like my XML structure is not being recognized by gamdSimulation.py (specifically the config.system object it expects).

My question:
What is the expected XML format for input (PDB/ForceField definitions, system parameters, etc.) so that gamdSimulation.py can parse it correctly?

I want to ensure my inputs are in the correct format without modifying the repo’s Python scripts. If there’s an example XML provided for RNA/DNA systems, I’d really appreciate being pointed to it.

Thank you for your time and for maintaining this project!

Best,
Tilak

[dyelar]

Hi Tilak, Input files is a top level directive outside of system. It also appears that you are using camel case in your xml tags, which doesn't match the gamd openmm xml specification. The examples found in https://github.com/MiaoLab20/gamd-openmm-examples should prove helpful to see how the xml file is organized. Best Wishes, Matthew Copeland

…

On Thu, Sep 4, 2025 at 12:50 AM ttpatel100 ***@***.***> wrote: *ttpatel100* created an issue (MiaoLab20/gamd-openmm#40) <#40> Hello, I am trying to run an RNA GaMD simulation using this repository, but I’m running into issues with the XML input. My current XML looks like this: <System> <InputFiles> <PDB>PDB_FILENAME</PDB> <ForceField>amber14/protein.ff14SB.xml</ForceField> <ForceField>amber14/DNA.bsc1.xml</ForceField> <ForceField>amber14/RNA.OL3.xml</ForceField> <ForceField>amber14/tip3p_standard.xml</ForceField> </InputFiles> <NonbondedMethod>PME</NonbondedMethod> <NonbondedCutoff>1.0</NonbondedCutoff> <Constraints>HBonds</Constraints> </System> When I try to run the simulation with run_gamd_interactive.py, I get warnings like: Warning: parameter in XML not found in config. Spelling error? InputFiles Warning: parameter in XML not found in config. Spelling error? ForceField ... Exception: No valid input files found. OpenMM simulation not made. It looks like my XML structure is not being recognized by gamdSimulation.py (specifically the config.system object it expects). My question: What is the expected XML format for input (PDB/ForceField definitions, system parameters, etc.) so that gamdSimulation.py can parse it correctly? I want to ensure my inputs are in the correct format without modifying the repo’s Python scripts. If there’s an example XML provided for RNA/DNA systems, I’d really appreciate being pointed to it. Thank you for your time and for maintaining this project! Best, Tilak — Reply to this email directly, view it on GitHub <#40>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABALA2IBLFDVIGD3TLGS6RT3Q7HIRAVCNFSM6AAAAACFSYKTHKVHI2DSMVQWIX3LMV43ASLTON2WKOZTGM4DEMRUHE4DMNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[ttpatel100]

Sounds good, I will check it out and return with any further inquiries.
Thank you so much!