GROMACS version: 2021.5
GROMACS modification: No
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Hello everyone,
I am new in gromacs. I am trying to learn this. Currently, I am working with POPC lipid membrane of 8000 lipids. System size is around 52 nm * 52 nm* 8 nm. System includes water and ions. I generated the system from charmm.gui with martini force field. In minimization mdp file I use rcoulomb = 1.2 and rvdw =1.2. When I ran this simulation I found some error and simulation did not run.
the error I found was:
There are 1 perturbed non-bonded pair interactions beyond the pair-list cutoff of 1.26 nm, which is not supported. This can happen because the system is nstable or because intra-molecular interactions at long distances are excluded. If the latter is the case, you can try to increase nstlist or rlist to avoid this.The error is likely triggered by the use of couple-intramol=no and the maximal distance in the decoupled molecule exceeding rlist.
After several times, I used 3.0 in both cases and simulation run successfully, however, my system did not minimized at all. The number of steps I used nsteps = 25000000.
What could be the way to resolve this issue? if anyone can help, It would be appreciated.
step6.0_minimization.mdp (1.7 KB)
step6.1_minimization.mdp (1.2 KB)