Issue running GROMACS Full MD Setup


#1

Molecular dynamics is new to me, so please forgive any novice errors. :wink:

I’m currently running MDWeb2, attempting to perform GROMACS Full MD Setup on chain A of the Piezo1 protein (PDBID:6B3R). However, despite multiple GROMACS setups, it consistently fails when heating the solvent to 300K.
Log file ends with the following error message:

Fatal error:
Too many LINCS warnings (1096)


#2

Hi Paul,

the system you are trying to setup is quite big for a web server like MDWeb. The solvent box for this system, even though you are just using the chain A, is really big, due to the extended conformation. A part from that, this PDB was solved using Electron Microscopy and has a resolution of 3.8A, requiring a careful checking before starting a MD simulation/setup. Just for example if you look at the structure checking section of MDWeb, it shows you 9 regions with missing residues in the protein, which should be modelled before starting the MD (and MDWeb is not able to do that). Now for the LINCS problems, they usually could be solved by playing with the minimization/equilibration time steps and configurations, but generally they are signs of an unstable system:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-June/089990.html
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

I would recommend you to start playing with MDWeb and Molecular Dynamics in general with a small, easy system, and then try it with more complex systems like the one you are dealing with, that will require some previous checking before starting the setup/MD simulation. And by the way, if you are interested on MD and biomolecular simulations, BioExcel is organizing lots of training events. Take a look at the web page! https://bioexcel.eu/

Hope it helps!

Thanks for your interest in our tool!


#3

Thanks for your help!