[gmx-users] Vacuum minimization of massive Protein:RNA complex.

[Miner, Jacob Carlson]

Can anyone recommend a good vacuum energy minimization method to minimize a Protein:RNA complex with over 300k atoms? (net charge about -800).



I have been able to get the system running (very slowly even on a 12-CPU-core machine) using a Gromacs version 4.5.5 of the standard minimization .mdp from the Lemkul Lab (using -DPOSRES on several of the heaviest atoms), but when I try to run an equivalent .mdp for version 5.1.4 I get the error:


"Domain decomposition does not work with nstlist=0"



Any recommendations? I just need to do a 'simple' minimization of my complex structure.


Thanks,


Jake Miner