On 30/09/2011 12:07 AM, oguz gurbulak wrote:
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 ?
You should read the notes and think about them. If they only pertain to
doing a simulation with the .tpr then you don't care. grompp can't
think for you, however.
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 ?
Make groups that have what you want in them. g_select, mk_ndx and
mk_angndx exist for this purpose. Sometimes a text editor is faster.
**
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 )
You need to make an index group when the default groups generated from
your structure file are insufficient for your needs.
Mark
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: -4.00e-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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