[gmx-users] editconf and g_rmsdist

[Enemark Soeren]

Dear GMX-users

 

I have a question about what happens when editconf is used to "box" a
molecule.

 

The reason I ask is because, I have used g_rmsdist in order to study how
a very small piece of a structure (100+ atoms) relaxes towards its
native state (given by NMR) after a small perturbation. After 10+ ns the
distrmsd has not been below 0.25 nm. 

Tracing back, I realized that the distrmsd was already 0.25 nm after I
inserted my NMR structure into the box in the first place!

 

I did the following:

 

 

1.     editconf -f NMR.gro -o boxed.gro -box 4 4 4

 

2.     /apps/gromacs4/bin/g_rmsdist -f boxed.gro -s NMR.gro -o
distrmsd-boxed-NMR

 

 

..

 

Select a group: 0

Selected 0: 'System'

..

 

3.     cat distrmsd-boxed-NMR.xvg 

 

# This file was created Fri Sep 18 13:02:06 2009

# by the following command:

# /apps/gromacs4/bin/g_rmsdist -f boxed.gro -s NMR.gro -o
distrmsd-boxed-NMR 

#

# /apps/gromacs4/bin/g_rmsdist is part of G R O M A C S:

#

# GROup of MAchos and Cynical Suckers

#

@    title "RMS Deviation"

@    xaxis  label "Time (ps)"

@    yaxis  label "RMSD (nm)"

@TYPE xy

@ subtitle "of distances between System atoms"

0  0.249025

 

 

 Just as a test, I tried also *NOT* to box the structure:

 

1.     editconf -f NMR.gro -o test.gro

2.     /apps/gromacs4/bin/g_rmsdist -f test.gro -s NMR.gro -o
distrmsd-boxed-NMR

 

...

Select a group: 0

Selected 0: 'System'

...

 

3.     cat distrmsd-boxed-NMR.xvg 

 

# This file was created Fri Sep 18 13:16:04 2009

# by the following command:

# /apps/gromacs4/bin/g_rmsdist -f test.gro -s NMR.gro -o
distrmsd-boxed-NMR

#

# /apps/gromacs4/bin/g_rmsdist is part of G R O M A C S:

#

# Giant Rising Ordinary Mutants for A Clerical Setup

#

@    title "RMS Deviation"

@    xaxis  label "Time (ps)"

@    yaxis  label "RMSD (nm)"

@TYPE xy

@ subtitle "of distances between System atoms"

0  1.83827e-08

 

 

 

 Why I am seeing this difference? Is it due to round-off's after the
transformation to center the molecule in the box? Or am I using
g_rmsdist wrongly?

 

 

 Best regards,

 Soren

 

 

 

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