Simulation accuracy of making it rain pipeline

[pablo-arantes]

Simulation accuracy of making it rain pipeline

[pablo-arantes]

Hi @rijuaxt,

Regarding your question, I have some points:

1. Making it rain IS NOT a MD engine. We prepare a Jupyter notebook scripts for running Molecular Dynamics simulations using OpenMM engine and AMBER and CHARMM force fields files on Google Colab. So, the accuracy should be related to OpenMM.

2. If you want to compare your obtained data on Making it rain notebooks with previous simulations from other engine, you should use the same parameters: Force Field, water model, box size, temperature, pressure and ions concentrations. Not only that, you should use the same barostat and so on...

3. I don't know which notebook you have been using. For example, if you are using the AMBER notebook (the first one), it works only for protein systems. If you have DNA, small ligand or a specific ion in your protein, the code will remove and keep only the protein for the simulation. It is clear on the notebook : "This is a Jupyter notebook for running Molecular Dynamics (MD) simulations using OpenMM engine and AMBER force field for PROTEIN systems."

Please, let me know if you have any question.

Thank you.

[rijuaxt]

I understand. I used protein-ligand colab notebook from github. My systems had proteins and ligand.

…

On Thu, Jul 7, 2022, 2:49 AM Pablo Ricardo Arantes ***@***.***> wrote: Hi @rijuaxt <https://github.com/rijuaxt>, Regarding your question, I have some points: 1. Making it rain *IS NOT* a MD engine. We prepare a Jupyter notebook scripts for running Molecular Dynamics simulations using OpenMM engine and AMBER and CHARMM force fields files on Google Colab. So, the accuracy should be related to OpenMM. 2. If you want to compare your obtained data on Making it rain notebooks with previous simulations from other engine, you should use the same parameters: Force Field, water model, box size, temperature, pressure and ions concentrations. Not only that, you should use the same barostat and so on... 3. I don't know which notebook you have been using. For example, if you are using the AMBER notebook (the first one), it works only for protein systems. If you have DNA, small ligand or a specific ion in your protein, the code will remove and keep only the protein for the simulation. It is clear on the notebook : *"This is a Jupyter notebook for running Molecular Dynamics (MD) simulations using OpenMM engine and AMBER force field for PROTEIN systems."* Please, let me know if you have any question. Thank you. — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ARJP5CFLHM6WJGPFM3Q4BQ3VSXWOZANCNFSM522VOFMA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[rijuaxt]

I have used same parameters for comparison. One point i needed know, which simulation box is used for protein-ligand jupyter Notebook?

[pablo-arantes]

Hi @rijuaxt,

If you are using the protein-ligand notebook, it's important to check which force field you have selected for the ligand. Are you using the same force field for the ligand that you used in your previous simulation?
The simulation box you should define the size in the Parameters to generate the topology cell. For the notebook we are using cubic box, as you can see in the Show 3D structure cell.

I hope it helps.

Thank you.