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On 30/09/2011 12:07 AM, oguz gurbulak wrote:
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<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>
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<br>
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.<br>
<br>
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<div><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>
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<br>
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.<br>
<br>
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**********<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>
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<br>
You need to make an index group when the default groups generated
from your structure file are insufficient for your needs.<br>
<br>
Mark<br>
<br>
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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>
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