[gmx-users] gromacs tools and namd

[oguz gurbulak]

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 ? 

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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

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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


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