Assistance Needed with MD Simulation of Large Molecule

User discussions
1

Dear Sir,
I hope this email finds you well. My name is LUKHMANUL HAKEEM K., and I’m a fourth-year undergraduate student currently conducting research in the Physicalorganic lab. I am reaching out to seek guidance regarding my recent attempts at molecular dynamics (MD) simulation using Gromacs.
To provide some context, I have followed a series of steps in setting up the MD simulation:

  1. I utilized the Antechamber tool to generate the force field parameters for our molecule.
  2. Subsequently, I employed the same tool to create force field parameters for acetone and solvated the molecule in acetone using a Leap script. This process generated the necessary prmtop and inpcrd files. ( I Follow this tutorial Tutorial 1 · Wiki · COBRAMM Development Group / cobramm · GitLab)
  3. I then used Acpype to convert the prmtop and inpcrd files to GROMACS format, resulting in topology, gro, em.mdp, md.mdp, and position.itp files.
  4. Afterward, I performed energy minimization on the structure and initiated an MD simulation for 10 picoseconds.
    I have uploaded all the files related to my simulation to a Google Drive folder, which you can access through the following link: acepdigromacs - Google Drive
    Given my limited experience, I am unsure whether the simulation setup and execution are correct and if the results can be considered valid. I would greatly appreciate it if you could review the files and provide me with feedback and guidance on any potential improvements or corrections needed to ensure the accuracy of my MD simulation.
    Looking forward to your guidance.

Warm regards,
LUKHMANUL HAKEEM K.

2

You need to check by yourself, go through the literature and understand about such system.
Anyhow, it would be better to keep your molecule at center.

3

Ok, Thank you sir.

4

Dear Lukhmanul,

A couple of considerations just by looking at the em.gro and md.gro files.

  1. The box is not solvated. Take a look at em.gro, for example. You have a few molecules here and there and most of the space is basically empty. By the look of it, I guess you used some tools that fill the space regularly in a crystal-like fashion. This doesn’t make sense in a solution, as your density is extremely low. Within my area of expertise, I would use gmx solvate (EDIT) to fill up to the brim the box.

  2. 10 ps are a very very short time. Even if the box was correctly solvated, that is a too short time to have actually some diffusion and relaxation of the box. Also, you are running an NVE simulation since you are not coupling neither the temperature nor the pressure. Is this the ensemble you are interested in?

EDIT Actually, it may be much convenient to use gmx insert-molecules rather than solvate, which requires the generation of a reference file within GROMACS directory. This may be very helpful as a guide.

5

Thank you sir.