Dear gmx users, after running grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr
I obtained: GROMACS: gmx grompp, VERSION 5.0 Executable: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/bin/gmx Library dir: /software/local/el6/INTEL/gromacs/5.0.0/intel-ompi-fftw-blas-lapack/share/gromacs/top Command line: grompp -f em.mdp -c COM_ions.gro -p COM.top -o em.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Setting the LD random seed to 2993272762 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA' Excluding 3 bonded neighbours molecule type 'DNA2' Excluding 3 bonded neighbours molecule type 'Protein3' Excluding 3 bonded neighbours molecule type 'Protein4' Excluding 3 bonded neighbours molecule type 'Protein5' Excluding 3 bonded neighbours molecule type 'Protein6' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' Excluding 1 bonded neighbours molecule type 'CL' Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 136 DNA residues There are: 1140 Protein residues There are: 557197 Water residues There are: 2152 Ion residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 5090256.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 216x216x216, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.27 NOTE 1 [file em.mdp]: This run will generate roughly 586540 Mb of data There was 1 note gcq#360: "error: too many template-parameter-lists" (g++) At the end I have em.tpr file but I am not sure if everything is ok. Any suggestions. best regards Urszula ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
