I am having a system with 450 Protein atoms and ~9000 water atoms. When I am trying to do the energy minimization step, it gives me hundreds of trajectory files (all .pdb with names like Step**_**.pdb). I am using gromos 53a6 force field with TIP4P water model. The error message also says something like (one atom moved too far during the domain decomposition steps) which is not quite visible in when I load the initial structure in VMD. The simulation completes sometimes but sometimes it also stops in the middle. Does anyone has any idea what can possibly be wrong, or any suggestion about how to remove this error?
Hi Swapnil,
This happens when your system turns unstable due to various reasons like
1. improper definition of topology parameters for any of the atoms in the entire system
2. improper definition of the step size, force parameters and others in .mdp file
3. due to small size of the solvent box
4. and others, which you may have to probe by noticing the error messages.
best regards,
Uday.
Hi Udaya,
Thanks. I saw that my Topology file was missing some information; I added it back and now this problem is solved. Thanks for your answer.
Apart from it, I also got to know that gromos53a6 force field is meant (only) for water model SPC or SPC/E. If one plans to run their system with geomos force field and TIP4P water model, they need to change a lot of things (ofcorse manually) in the forcefield.
Best,
Swapnil
change the pressure coupling system in .mdp files.
if it is parrinello-rahman change it to berendsen
Faeze Sadat: Actually that problem is solved now; I am stuck somewhere else. PR pressure coupling also works, but the problem is they suggest not to add additional parameters/atomtypes into the existing forcefield file. So, I think, I will not be able to run the simulation by adding the TIP4P water model parameters into the gromos53a6 force field file (although I came to know that TIP4P water model can be run with gromos43a1 force field).
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