[gmx-users] Re: PE compressing

Vitaly Chaban vvchaban at gmail.com
Mon Jul 26 05:24:05 CEST 2010

Dear Moeed:

The simulation has given you CONFOUT.GRO with new [good] density. I
guess this is the only output file you really need here. If you want a
detailed trajectory, please just use:
nstxout             =  something
nstvout             =  something
nstfout             =  something
nstxtcout         =  something

You may also use g_energy to look at the evolution of the PE density,
energies, etc.

As for the pbc option, this is just an erratum. You are right.


> 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.

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