[gmx-users] Question regarding tpr files and rmsd
Mark Abraham
mark.abraham at anu.edu.au
Thu Aug 12 16:04:20 CEST 2010
----- Original Message -----
From: Bernhard Knapp <bernhard.knapp at meduniwien.ac.at>
Date: Thursday, August 12, 2010 23:28
Subject: [gmx-users] Question regarding tpr files and rmsd
To: gmx-users at 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:
>
> [bknapp at 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?
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 remaining difference should be attributable to the difference between whatever coordinate changes pdb2gmx is making (I can't tell what, if any) based on the two slightly different starting points - but subjecting both to rounding to .gro precision. This last point explains why they're so similar, I expect.
Mark
> example:
> [bknapp at 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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