Fatal Error during nvt run

User discussions
1

GROMACS version: 2022.4
GROMACS modification: Yes/No
Hello experts,
While using Command line:
gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

I am facing a Fatal Error.
Program: gmx grompp, version 2022.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2192)

Fatal error:
Cannot find position restraint file restraint.gro (option -r).
From GROMACS-2018, you need to specify the position restraint coordinate files
explicitly to avoid mistakes, although you can still use the same file as you
specify for the -c option.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

Kindly help!

2

Hi prsinha,

It seems that your topology file prescribes some position restraints; have a look here: https://manual.gromacs.org/current/reference-manual/functions/restraints.html

The simplest way to solve this error is to do what gmx grompp suggests, that is to use em.gro as reference configuration:
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr

Otherwise, in case you don’t want to use em.gro as reference, you need to build a reference configuration for the restrained positions to provide to gmx grompp.

3

Okay thank you sir I have successfully generated my files.

4

This command is not working fatal error came
Fatal error:
Invalid T coupling input: 3 groups, 2 ref-t values and 2 tau-t values
by this command gmx grompp -f nvt.mdp -c em.gro -r em. gro -p topol.top -n index.ndx -o nvt.tpr
I done all steps related to equilibrium but this error i can not handle it can you plz help me

5

Have a look at your temperature coupling settings in the MDP file. The error message says that you have three temperature coupling groups, but only two reference temperatures and two time constants. See https://manual.gromacs.org/current/user-guide/mdp-options.html#temperature-coupling for more information.

6

System containg peptide and solvent. I changed nvt.mdp file tc-grps but it is not working fatal error showing.

7

We cannot help you without the relevant file contents. Please copy your temperature coupling settings here.