Hello,
Currently i've been running a protein-ligand simulation for 20ns. But unfortunately i got some error while doing NVT and NPT equilibration. I got warning about system exploding and 1,4 interactions.
I read a suggestion about changing the 'couple-intramol' parameters to 'Yes', but my .mdp file doesn't have that parameters.
There's another recommendation about changing the table extension but i can't figure it out how to do it.
So, anyone knows how to change the table extension or any other suggestion method that i can do about this error? I attach picture that show the warning in my simulations.
Thank you in advance!
Just go through this tutorial (http://www.mdtutorials.com/gmx/complex/index.html) and modify the parameters in your mdp files according to the gromacs version and the forcefield you're using (Gromacs reference manual).
It's also good to take a quick look into the published literature (of your target protein) that used MD simulation in their work.
Hi,
For this
when you create a TPR file, GMX also creates an output file (mdout.log something like that), which contains all the parameters that GMX is going to use for the simulation. You can check in that file what parameter value has been set. Since GMX uses many default parameter values, they are not present in the MDP file (most of the time).
If you are having this kind of issue, it means either your ligand parameters are not good or you are making some fundamental mistake in the MDP file. Please take a good look at your ligand parameters, and it is often better to use already reported ligand parameters, if available.
I don't think you need to change the table parameters like somewhere else suggested that may be for something else as you wrote
Good luck.
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