<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear All,<br><br>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 ? <br><br>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 ? <br><br>**********<br>Select a reference group and 1 group<br>Group 0 ( System) has 3760 elements<br>Group 1 ( Other) has 3760 elements<br>Group 2
( A) has 380 elements<br>Group 3 ( B) has 3000 elements<br>Group 4 ( C) has 380 elements<br>**********<br><br>However, do I need to generate a .ndx file for each gmx analysis tools ?<br><br>make_ndx -f .tpr -o .ndx ( for example )<br><br>Thank you very much for your attention.<br><br>Best regards<br><br>*************<br>Generated 105 of the 105 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 105 of the 105 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'molecule0'<br>Excluding 3 bonded neighbours molecule type 'molecule1'<br>Excluding 3 bonded neighbours molecule type 'molecule2'<br><br>NOTE 1 [file
gromacs.top, line 292]:<br>System has non-zero total charge: -4.000000e-03<br><br>NOTE 2 [file gromacs.top]:<br>The largest charge group contains 14 atoms.<br>Since atoms only see each other when the centers of geometry of the charge<br>groups they belong to are within the cut-off distance, too large charge<br>groups can lead to serious cut-off artifacts.<br>For efficiency and accuracy, charge group should consist of a few atoms.<br>For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>NOTE 3 [file gromacs.top]:<br>The largest charge group contains 14 atoms.<br>Since atoms only see each other when the centers of geometry of the charge<br>groups they belong to are within the cut-off distance, too large charge<br>groups can lead to serious cut-off artifacts.<br>For efficiency and accuracy, charge group should consist of a few atoms.<br>For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br><br>Analysing residue
names:<br>There are: 1040 Other residues<br>Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<br>Number of degrees of freedom in T-Coupling group rest is 11277.00<br>Largest charge group radii for Coulomb: 0.535, 0.535 nm<br>Calculating fourier grid dimensions for X Y Z<br>Using a fourier grid of 21x21x168, spacing 0.119 0.119 0.119<br>Estimate for the relative computational load of the PME mesh part: 0.34<br>This run will generate roughly 89 Mb of data<br>There were 3 notes<br>Are these notes<br><br><br>*********</div></div></body></html>