Equilibration step does not work

User discussions
1

Hello Gromacs users:

I have created a CG-vesicle using CHARMM-GUI and I have downloaded the gromacs file and the README with the minimization, equilibration and production steps. The minimization worked ok:

step6.0 - soft-core minimization

gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_charmm2gmx.pdb -p system.top -r lipidtail_posres.pdb -n index.ndx
gmx mdrun -deffnm step6.0_minimization

step6.1

gmx grompp -f step6.1_minimization.mdp -o step6.1_minimization.tpr -c step6.0_minimization.gro -p system.top -r lipidtail_posres.pdb -n index.ndx
gmx mdrun -deffnm step6.1_minimization

But the equilibration does not work:

gmx grompp -f step6.2_equilibration.mdp -o step6.2_equilibration.tpr -c step6.1_minimization.gro -p system.top -r lipidtail_posres.pdb -n index.ndx

It gives me this error:

Fatal error:
Can not invert matrix, determinant is zero

Does someone know what can I do?

Thank you in advanced.

2

Hi,
please state which GROMACS version are you using, what ( gmx grompp or gmx mdrun) gives error and what is the message in the standard output.
Kind regards
Alessandra

3

Thank you for your reply.
I am using the Gromacs 2020.1 version
When we execute this:
gmx grompp -f step6.2_equilibration.mdp -o step6.2_equilibration.tpr -c step6.1_minimization.gro -p system.top -r lipidtail_posres.pdb -n index.ndx
The error message is this one:
Fatal error:
Can not invert matrix, determinant is zero

Best regards

4

Hi,
It can be a problem in the definition of your box. Can you check that your gro file contains all the correct information (see here for file format http://manual.gromacs.org/current/reference-manual/file-formats.html?highlight=coordinate%20file#gro).
Also check your lipidtail_posres.pdb. Note you can use step6.1_minimization.gro (in place of lipidtail_posres.pdb) for the option -r .
Last, I would like to try to reproduce the error. Can you provide me a link to your input? Thank you

Alessandra

5

I attached here the files so you can reproduce the error and maybe you could find the solution because I still have not solved the problem.

Best regards.

6

You need to include the full toppar directory, otherwise grompp doesn’t have the force field files required by the topology.

7

Thank you for your reply. Here I attached the toppar directory.

Best regards.