I am trying to investigate a membrane proteins influence on a lipid bilayer using molecular dynamics. I am new to MD and trying to run my first simulation. I have built the simulation input files using CHARMM-GUI and now I am using gromacs to perform the simulation.
CHARMM-GUI provides these commands to get gromacs to perform the initial minimization
gmx_d grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top gmx_d mdrun -v -deffnm step6.0_minimization
The first command runs fine. The second command starts the minimization, but at step 15 it freezes.
... Step 15, time 0.015 (ps) LINCS WARNING relative constraint deviation after LINCS: rms -nan, max 0.098209 (between atoms 16596 and 16597) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 15683 15684 39.2 0.1109 0.1121 0.1111 15683 15685 38.4 0.1115 0.1107 0.1111 16596 16597 72.1 0.1111 0.1220 0.1111 16640 16642 35.3 0.1116 0.1120 0.1111 16643 16644 51.9 0.1108 0.1136 0.1111 16643 16645 47.2 0.1114 0.1079 0.1111
In step 15, the rms is -nan, so I'm guessing that is the problem, and I am assuming that is coming from the difference between the "current" and "previous" is greater than constraint length like on this line here
16596 16597 72.1 0.1111 0.1220 0.1111
The problem is I don't have any intuition on how to fix it? The pdb file is a homology model from phyre without any modification other than adding a single chain id to all the residues. I'm using a 1 to 1 POPC and DOPC in both membrane layers with a CHARMM36m force field.
The previous steps also throw LINCS warnings about bonds exceeding 30 degrees, however they produce a real value for rms.
I've counted on tutorials to get this far and would appreciate some suggestions or good resources I can use to continue my simulation.