normal "LINCS WARNING" for EINeDyn in the protein tutorial

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7 months 5 days ago #7993 by lanselibai
Dear Martini experts,

I am following the instructions for 1A8G protein at
cgmartini.nl/index.php/tutorials-general...n-gmx5/proteins-gmx5

Because I am using Gromacs 2018, so I added "-r structure.gro" in the grompp commend when "define = -DPOSRES" exists in the .mdp file. For example:

gmx grompp -f equilibration-posres-10fs.mdp -r minimization.gro -c minimization.gro -p system.top -o equilibration-posres-10fs.tpr

Everything else is kept the same as shown in the "COMMANDS".file provided. And I used all the initial files provided (e.g. .martinize.py, martini_v2.2.itp, mdp files).

However, the RMSD would always jump after 10 ns for all the three runs (no elastic, with elastic, EINeDyn). The "no elastic" and "with elastic" could finish the 20 ns production runs successfully, while the "EINeDyn" will encounter "LINCS WARNING" at around 15 ns.
github.com/lanselibai/martini/blob/maste.../LINCS%20WARNING.jpg

The RMSD plot is here
github.com/lanselibai/martini/blob/maste...PlotCompare/RMSD.jpg

I have attached my files to the github. Please let me now if you could not see them.
github.com/lanselibai/martini/tree/maste...116_protein_tutorial

So how can I run the simulation smoothly?

Thank you.

Yours sincerely
Cheng

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6 months 2 weeks ago #8026 by Pim
Hi Cheng,

Adding the coordinates in the -r flag is right for Gromacs2018.

The RMSD jumps look like they are caused by the protein crossing the periodic boundaries. This is not a problem. You can fix it by following the steps in the COMMANDS file provided. Did you try that (specifically the -nojump lines?).

For the LINCS warnings it is difficult to say, but maybe you are just unlucky with your simulation. Restarting the simulation might already solve the problem, otherwise try again with a different random seed (-seed) in the gmx solvate step.

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