[gmx-users] editconf and g_rmsdist
Enemark Soeren
chees at nus.edu.sg
Fri Sep 18 09:53:26 CEST 2009
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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