Assistance Needed: Issue with Simulation Setup and Visualization

User discussions
1

Dear Sir,
I hope this email finds you well. I am currently facing an issue with my simulation setup and visualization process. To provide context, I have been working on creating a cubic box with acetone solvent for simulation purposes. Initially, I obtained the GROMACS topology using the ligand reader and force field converter in CHARMM-GUI. Subsequently, I constructed a cubic box and inserted 3000 acetone solvent molecules into it using the command “gmx insert-molecules -ci acetone.gro -nmol 3000 -o solacetone.gro -box 10.00 10.00 10.00”. Following this, I performed energy minimization. However, upon attempting to visualize the em.gro and em.trr files, I noticed an unexpected abundance of lines when loading em.trr. I’m unsure why this is occurring and if the steps I’ve followed are correct. For your convenience, I have attached a link to all files present in my folder and included a VMD image. Your assistance in resolving this issue would be greatly appreciated.
Looking forward to your guidance.
https://drive.google.com/drive/folders/19cW4xIBjBpU7MDexDC9ptSdfarcvZbuk?usp=sharing

image
image849×808 353 KB

Best regards,
LUKHMANUL HAKEEM K.

2

this is PBC effect, you need to remove the PBC effect using [gmx trjconv](https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html)

3

Dear Sir,
Thank you so much sir for your reply.