How do I minimise energy for DOPC lipid bilayer?

30 April 2020 0 6K Report

I am trying to minimise the energy for a DOPC lipid bilayer on gromacs 2020.01. I have done the following steps to prepare for energy minimsation:

1. Generated lipid bilayer using Charm-Gui Membrane Builder (121 lipids/leaflet, 40 waters/lipid, no ions as DOPC is neutral). I am using TIP3P waters and the slipids FF from Jambeck and Lyubartsev

2. I created a .gro, .top and posre.itp file using pdb2gmx

3. Lipid bilayer was centered

4. .tpr file was generated using grompp

5. I then tried to run >gmx mdrun -v -deffnm dopc-min but Fmax appears to be infinite at atom 9096 (see attached).

Can I simply remove the atom from the dopc-min.tpr file and try to run it again (which I tried and it didn't work)? How can I ensure the atoms are not overlapping?

Is this problem due to an issue in the .mdp file? The last time I tried this was on gromacs 5.04 and I am currently using gromacs 2020.01. Would the .mdp file still work?

Thank you very much in advance!

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