[gmx-users] make_edi fails with multiple eigenvectors for -linfix and -linacc

Carsten Kutzner ckutzne at gwdg.de
Thu Dec 24 11:59:03 CET 2009

Hi Chris,

On Dec 23, 2009, at 9:06 PM, chris.neale at utoronto.ca wrote:
> Hello,
> I am having trouble getting make_edi -linfix to work with multiple eigenvectors.
> This works for a single EV:
> $ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f ../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix "1"  -linstep "0.0001"  -outfrq 50
> And throws an error for:
> $ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f ../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix "1 2"  -linstep "0.0001 0.0001"  -outfrq 50
> "Error in the list of eigenvectors for -linfix at pos 2 with char"
From a quick look at the code it seems to me that the whitespace is the problem here.
Try to replace it with a comma "," 

If that still does not work you can also call make_edi several times and after that concatenate the .edi
files - this should lead to the same result.

> Here is the output, first for the error, then for the single EV that works, then showing that I get the same error with -linacc
> I included quotes around the -linfix list and ran it directly from the command line (no script) to be entirely sure that the quotes were being passed to gromacs and not interpreted by the shell. In any event, without the quotes it is not interpreted as a string and complains about the unknown argument "2".
> There is an old mailing list post that suggests my intnded usage is expected to work: http://lists.gromacs.org/pipermail/gmx-users/2005-August/016638.html
> Is the WHATIF software still 100% compatible with gromacs? I suppose that I could just skip make_edi all together in favour of WHATIF if the problem here is not in my usage and is not easily repaired.
99% I would say. One entry (the total number of atoms in the protein) became obsolete for Gromacs,
plus the magic number increased. You can easily change that in the edi file that comes from WHATIF if
you compare that with a gmx 4.0 edif file. 

Have a merry Christmas,

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