Max Tolentino

7 Questions 4 Answers 0 Followers

Questions related from Max Tolentino

How to solve error in Gromacs: "Fatal error: Can not invert matrix, determinant is zero"?

Hi everyone! The said fatal error stopped my run altogether. It did, however, started minimization. Any idea how to solve this? Thank you so much!

20 May 2021 4,557 1 View

Gromacs on HPC error: "Increase box size or decrease rlist".What do I do?

Hi everyone! I'm doing an MD run on Gromacs on HPC and the error attached below popped up. The original rlist was 1.2, and I tried decreasing it to 1, then 0.5, then 0.1, but the same error still...

19 May 2021 2,973 3 View

All files that needed to be combined start at the same time or time frame in MD. How to fix this?

Hi, I'm working on Gromacs on HPC to run MD simulations. I tried combining individual files from step 5, which is the MD production step, using the gmx trjcat command so that I could post-process...

15 April 2021 1,638 2 View

How to construct a Complex Langevin phase diagram?

A little background: I am an undergraduate student, a biochemistry major with little to no background in bioinformatics. We're only allowed to choose dry lab topics for our thesis since we cannot...

11 March 2021 8,352 1 View

Can I use the CHARMM GUI input files for Gromacs in HPC?

Good day everyone! I am a Biochemistry undergraduate in the Philippines and to be very honest, we have no background in bioinformatics since we really focused on wet lab techniques + theory. Due...

16 February 2021 3,766 4 View

Can I use GROMACS for field-theoretic simulation of copolymers?

I need to know if I can use GROMACS instead of LAMMPS for my undergraduate thesis wherein I will generate phase diagrams of copolymers using FTS. Thank you so much!

23 November 2020 3,861 3 View

"Fatal error: Group SOLV referenced in the .mdp file was not found in the index file." Help with SLURM HPC

Hi everyone, I hope you're all safe and doing great. So I cannot install my Gromacs in my laptop, so I used SLURM HPC instead for MD. The Gromacs input files that I used were generated in...

01 January 1970 2,114 1 View