[gmx-users] PE compressing

Moeed lecielll at googlemail.com
Sun Jul 25 20:50:57 CEST 2010

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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