Dear Dr. Chaban,<br><br>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:<br>
processing topology...<br>Analysing residue names:<br>There are: 240 OTHER residues<br>There are: 0 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Other...<br>Calculating fourier grid dimensions for X Y Z<br>
Using a fourier grid of 270x250x250, spacing 0.119 0.120 0.120<br>This run will generate roughly 2 Mb of data<br><br>Generating 2Mb !!!! This is concerning since I am running NPT for 2ns. <br><br>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.<br>
<br>Please help me with this matter. <br><br>Thanks :)<br><br><br>