Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly.
You can also override the warnings with the -maxwarn <number> option in grompp. Carsten On Oct 29, 2012, at 3:52 PM, Albert <mailmd2...@gmail.com> wrote: > hello: > > I am generating a .tpr file for proten/ligand system, but it has so much > warnings: > > > NOTE 1 [file md.mdp]: > nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting > nstcomm to nstcalcenergy > > > NOTE 2 [file md.mdp]: > leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 > > Generated 23436 of the 23436 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 20254 of the 23436 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein' > turning all bonds into constraints... > Excluding 3 bonded neighbours molecule type 'LIG' > turning all bonds into constraints... > Excluding 3 bonded neighbours molecule type 'POPC' > turning all bonds into constraints... > Excluding 2 bonded neighbours molecule type 'SOL' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'NA' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'CL' > turning all bonds into constraints... > Setting gen_seed to 6947582 > Velocities were taken from a Maxwell distribution at 300 K > > NOTE 3 [file complex.top]: > The largest charge group contains 12 atoms. > Since atoms only see each other when the centers of geometry of the charge > groups they belong to are within the cut-off distance, too large charge > groups can lead to serious cut-off artifacts. > For efficiency and accuracy, charge group should consist of a few atoms. > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. > > Number of degrees of freedom in T-Coupling group Protein_LIG is 9475.34 > Number of degrees of freedom in T-Coupling group POPC is 33353.66 > Number of degrees of freedom in T-Coupling group Water_and_ions is 53973.00 > Largest charge group radii for Van der Waals: 0.299, 0.299 nm > Largest charge group radii for Coulomb: 0.299, 0.299 nm > > NOTE 4 [file md.mdp]: > The sum of the two largest charge group radii (0.597592) is larger than > rlist (1.000000) - rvdw (1.200000) > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists