Dear All, I'm trying to use some gmx 4.5 tools like g_rdf, g_order, g_msd, g_hbond. To do it I composed a top file using psf and dcd files with topotools1.2 in vmd and generated a tpr file but also I saw some notes below on terminal. Do any of these notes will cause a problem when making analysis ? Should I consider them ?
For example I want to calculate rdf for atom-atom or atom-molecules not for groups. What should I do generally to make analysis for atoms and molecules ? ********** Select a reference group and 1 group Group 0 ( System) has 3760 elements Group 1 ( Other) has 3760 elements Group 2 ( A) has 380 elements Group 3 ( B) has 3000 elements Group 4 ( C) has 380 elements ********** However, do I need to generate a .ndx file for each gmx analysis tools ? make_ndx -f .tpr -o .ndx ( for example ) Thank you very much for your attention. Best regards ************* Generated 105 of the 105 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 105 of the 105 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'molecule0' Excluding 3 bonded neighbours molecule type 'molecule1' Excluding 3 bonded neighbours molecule type 'molecule2' NOTE 1 [file gromacs.top, line 292]: System has non-zero total charge: -4.000000e-03 NOTE 2 [file gromacs.top]: The largest charge group contains 14 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. NOTE 3 [file gromacs.top]: The largest charge group contains 14 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. Analysing residue names: There are: 1040 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 11277.00 Largest charge group radii for Coulomb: 0.535, 0.535 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 21x21x168, spacing 0.119 0.119 0.119 Estimate for the relative computational load of the PME mesh part: 0.34 This run will generate roughly 89 Mb of data There were 3 notes Are these notes *********
-- 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
