Re: [gmx-users] error gcq#360
On 6/26/15 9:15 AM, Urszula Uciechowska wrote: 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: 136DNA residues There are: 1140Protein residues There are: 557197 Water residues There are: 2152Ion 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. gcq are GROMACS cool quotes and serve no functional purpose except the amusement of the user. There is no error here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
[gmx-users] error gcq#360
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: 136DNA residues There are: 1140Protein residues There are: 557197 Water residues There are: 2152Ion 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.
Re: [gmx-users] error gcq#360
Hi, There's no problem - that's just a fun Gromacs Cool Quote (i.e. gcq), as the tools often print at the end of their run. This one is perhaps not a good wording! (There are ways to turn them off, if they annoy people.) Mark On Fri, Jun 26, 2015 at 3:24 PM Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: 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: 136DNA residues There are: 1140Protein residues There are: 557197 Water residues There are: 2152Ion 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. -- 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.
