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How to fix this error in equilibration steps of MD simulation which says 59196 atoms are not part of any of T-coupling groups ?
If you look in the .mdp file, the T-coupling groups you’re using are set using tc-groups. The error means those 59196 are not included in any of those groups. You’ll need to identify what those missing atoms are and either choose the existing groups that include those atoms or create a new index file to define new groups that include those atoms (you can use gmx make_ndx to do so)
Thank kris for your response . I retried the gmx make_ndx -f em.gro -o index.ndx was created this time. I create the system and protein group besides creating the protein and ligand group . As my system is neutral I am unable to create the water and ions system after creating protein and system group I wrote this protein - system group. now again fatal error came which says atom1 in multiple T-coupling groups.kindly help me in fixing this error .
Waiting for your kind response.
The error is due to the protein atoms being included in both groups. If you have the protein and ligand in one group, the second group should just be all the other atoms (if there aren’t ions in the system, then the second group would just be the solvent).
Also, the “system” includes every atom, so making a group including the system and protein in a group is double counting the protein atoms. Using make_ndx should include a list of the existing groups and the number of atoms in each group as part of the output so an easy check to see if everything is accounted for is to see if the atoms included in your groups all add up to the atoms in the system.
Thank you for your kind response . Now I created second group which only consists of SOL molecule. Now the file .tpr is generated
Is this correct ?
Thank you for your response
Regarding that specific error, you should be fine now
I want to run MD production for 100ns what changes I have to make and in which file ? Do I have to make changes in nvt.mdp and npt.mdp file besides md.mdp file? I tried to run MD for 100 ns by making changes in md.mdp file but the output obtained in 10 ns. I shall be thankful to you for your kind response.
md.mdp is the only one you should need to adjust. You may need to double check the number of steps (nsteps) and the time per step (dt) is set correctly
Thanks Karis for your response . In the MD production steps these two warning came. These two warnings are
warning1(file md.mdp)
For proper integration of Parrinello-Rahman barostat, tau-p (2) should be at least 20 times larger than nstcouple*dt (0.4)
Warning2[file topol.top, lines 83963]
The bond in molecule-type Protein_chain_A between atom 10 CG and 11 OD1 has an estimated oscillational period of 2.2e-02 ps, which is less than 5 times the time setup of 2.0e-02 ps.
Maybe you forgot to change the constraints md option.
kindly help me in resolving this warning. I shall be grateful to you .
waiting for your kind response.
I’m not familiar with fixing these errors specifically, but based on users who experienced similar errors in the past, you may need to adjust the parameters in your mdp file according to the warnings you got. ([gmx-users] Martini in Gromacs), ([gmx-users] Tau-t should be at least 20 times larger than nsttcouple*dt). Since it seems you’ll have to lower the time setup (dt) for the second warning, and considering how that also affects the first warning, that may be the most straightforward way to adjust the settings, just keep in mind how much you need to increase nsteps for the simulation to run for the amount of time you need