[gmx-users] gromacs tools and namd

[Mark Abraham]

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: -4.000000e-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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