- Original Message -
From: Bernhard Knapp
Date: Thursday, August 12, 2010 23:28
Subject: [gmx-users] Question regarding tpr files and rmsd
To: gmx-users@gromacs.org
> 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".
Sure. GROMACS-written PDB files contain no connectivity data. .tpr files do.
> The average
> difference (over 10 ns) between the xvg file based on the
> tpr and on the pdb is 0.01447971.
Probably quite a reasonable difference in the average RMSD (in nm), given the
pdb approximates the floating-point numbers in the .tpr with only 3 decimal
points (in Angstrom)
> 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"
> 0.000
> 0.0005041 |0.0000.0005046
> 3.000
> 0.1072081 |3.0000.0981387
> 6.000
> 0.1281023 |6.0000.1207779
> 9.000
> 0.1452615 |9.0000.1351306
> ...
>
>
> My questions are now:
>
> - Why are the xvg files different if they are based on the tpr
> and on the pdb file?
PDB has more limited precision than the .tpr, and if you're fitting to their
structure, you'll get slightly different results.
> - What is the more appropriate way to calculate the rmsd?
Depends what you're trying to measure - but I'd argue there shouldn't be a
significant difference between these two.
> - 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
It's about the best you can do. IIRC, the firstframe.pdb will have higher
precision than the first frame of the .xtc, typically, and so produce a .tpr
closer to the original.
The procedure below is unnecessarily regenerating water. Use pdb2gmx to
generate the .top, and then simply use grompp to combine .mdp, .top and
whichever source of the first frame you choose.
> 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)
You fitted and analyzed with respect to Protein, so the re-generation of the
water should have no effect here. The
