Dear Dr. Chaban, Thank you for your attention. Actually with the revised mdp file you sent me and the initial configuration of my 8PE system, I tried to compress the system. The simulation tales very long and produces nothing. grompp is giving me: processing topology... Analysing residue names: There are: 240 OTHER residues There are: 0 PROTEIN residues There are: 0 DNA residues Analysing Other... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 270x250x250, spacing 0.119 0.120 0.120 This run will generate roughly 2 Mb of data
Generating 2Mb !!!! This is concerning since I am running NPT for 2ns. I just used the mdp file and the only thing I changed was pbc=full. Actually I tried this option but grompp gave a warning saying that I shoudl use xyz option. I did not even find "full" optioon in the manual for pbc! I am wondeig how you could run the simulation with this setting. Please help me with this matter. Thanks :)
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