Dear users
Due to a hard disk crash we lost several md simulations. Fortunalty we
have backup copies of the trajectry files (xtc format) and structure
files of the first frame of the simulation (created via trjconv -b 0 -e
0 -f myName.md.trr -o myName.md.firstframe.pdb -s myName.md.tpr). We
do not have the tpr files which we usually used for example for the
rmsd calculations. We found that the -s option of g_rms does not only
take tpr files but also pdb files, however when I compare the resulting
xvg files the values are slightly different and I get a warning
"Warning: if there are broken molecules in the trajectory file, they
can not be made whole without a run input file". The average difference
(over 10 ns) between the xvg file based on the tpr and on the pdb is
0.01447971.
Example for the 2 file:
[bkn...@quovadis02 test]$ sdiff rmsd.pdb.xvg rmsd.tpr.xvg | less
# This file was created Thu Aug 12 11:23:09 2010 | # This
file was created Thu Aug 12 11:22:06 2010
# by the following command: # by the
following command:
# g_rms -f 1mi5_A6D.md.xtc -s 1mi5_A6D.md.firstframe.pdb -o r | # g_rms
-f 1mi5_A6D.md.xtc -s 1mi5_A6D.md.tpr -o rmsd.tpr.xvg
# #
# g_rms is part of G R O M A C S: # g_rms
is part of G R O M A C S:
# #
# GROtesk MACabre and Sinister | # S C
A M O R G
# #
@ title "RMSD" @
title "RMSD"
@ xaxis label "Time (ps)" @
xaxis label "Time (ps)"
@ yaxis label "RMSD (nm)" @
yaxis label "RMSD (nm)"
@TYPE xy @TYPE xy
@ subtitle "Protein after lsq fit to Protein" @
subtitle "Protein after lsq fit to Protein"
0.0000000 0.0005041 |
0.0000000 0.0005046
3.0000000 0.1072081 |
3.0000000 0.0981387
6.0000000 0.1281023 |
6.0000000 0.1207779
9.0000000 0.1452615 |
9.0000000 0.1351306
...
My questions are now:
- Why are the xvg files different if they are based on the tpr and on
the pdb file?
- What is the more appropriate way to calculate the rmsd?
- Just if the more appropriate way is the tpr file: Is it valid to
recreate the tpr file via grompp solely on the firstframe.pdb and the
xtc of the trajectory? eg via
pdb2gmx -f 1mi5_A6D.md.firstframe.pdb -o 1mi5_A6D.md.firstframe.pdb.gro
-p 1mi5_A6D.md.top
editconf -f 1mi5_A6D.md.firstframe.pdb.gro -o
1mi5_A6D.firstframe.cube.pdb -bt cubic -d 2.0
genbox -cp 1mi5_A6D.firstframe.cube.pdb -cs spc216.gro -o
1mi5_A6D.firstframe.water.pdb -p 1mi5_A6D.md.top
grompp -f md.mdp -c 1mi5_A6D.firstframe.water.pdb -p 1mi5_A6D.md.top -o
1mi5_A6D.md.RECREATED.tpr
then the average difference between the xvg file based on the tpr and
the recreated tpr is 1.4865E-05 (which is much more similar however
still not identical)
example:
[bkn...@quovadis02 test]$ sdiff rmsd.tprRECREATED.xvg rmsd.tpr.xvg | less
# This file was created Thu Aug 12 11:59:23 2010 | # This
file was created Thu Aug 12 11:22:06 2010
# by the following command: # by the
following command:
# g_rms -f 1mi5_A6D.md.xtc -s 1mi5_A6D.md.RECREATED.tpr -o rm | # g_rms
-f 1mi5_A6D.md.xtc -s 1mi5_A6D.md.tpr -o rmsd.tpr.xvg
# #
# g_rms is part of G R O M A C S: # g_rms
is part of G R O M A C S:
# #
# GROup of MAchos and Cynical Suckers | # S C
A M O R G
# #
@ title "RMSD" @
title "RMSD"
@ xaxis label "Time (ps)" @
xaxis label "Time (ps)"
@ yaxis label "RMSD (nm)" @
yaxis label "RMSD (nm)"
@TYPE xy @TYPE xy
@ subtitle "Protein after lsq fit to Protein" @
subtitle "Protein after lsq fit to Protein"
0.0000000 0.0022253 |
0.0000000 0.0005046
3.0000000 0.0981661 |
3.0000000 0.0981387
6.0000000 0.1207914 |
6.0000000 0.1207779
9.0000000 0.1351781 |
9.0000000 0.1351306
...
cheers
Bernhard
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