GROMACS modification: Yes/No
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I am solvating a bilayer with TIP4P/2005 water. I generated the initial configuration using the packmol software. But during the energy minimisation the simulation stops with too many LINCS warning. The warnings arises because of water molecules. The lipid bonds are breaking too. How to perform the energy minimisation for such systems.
That sounds strange. LINCS should not be used for water, that is always SETTLE. Are you sure LINCS is used for water?
My guess is that the quality of your initial state is so bad that it can not be energy minimized.
And why do you want to use TIP4P/2005 with a membrane? TIP4P/2005 is incompatible with most force fields.
Thank you Hess for your reply and indeed the initial state had a problem. Actually, I made a mistake in defining the new atom types and pairtypes in the parameter file. That is why the system was facing extremely larger forces and was unable to energy minimize. Now, I have corrected those non-bonded force field parameters, after calculating it for the new atom type (the interaction with SPC was given and I modified accrodingly) and voila it worked. I really will appreciate any suggestions and comments in this direction and the pitfalls that I might have overlooked.