SV: SV: SV: [gmx-users] g_saltbr

Tsjerk Wassenaar tsjerkw at
Wed Dec 2 19:29:29 CET 2009


Of course the real answer is in the code...

  if (bSep) {
    for(i=0; (i<ncg); i++)
      for(j=i+1; (j<ncg); j++) {
        if (nWithin[i][j]) {
          fp=xvgropen(buf,buf,"Time (ps)","Distance (nm)");

So, a file is opened for each combination of charge(d) groups for
which the distance is lower than the cut-off, at least once in the
trajectory. The label is a property of the charge group, and is set
somewhere before:


Althogether, this just means that you have multiple charge(d) groups
per residue, which are assigned the same label. Let's see, a phosphate
and a choline, two residues, 2*2=4 possible salt bridges between them.
Seems to add up, doesn't it? Probably should be considered a bug
though. Better file it...



On Wed, Dec 2, 2009 at 7:10 PM, Justin A. Lemkul <jalemkul at> wrote:
> Sarah Witzke wrote:
> <snip>
>> In each of the files are a set of distances as a function of time - it
>> does not seem that strange, that the size is equal then.
>> When I plot for instance the four .xvg files mentioned above I get four
>> different curves. Also "diff" lists that every line is different.
>> I really don't understand what I'am doing wrong.
> I don't know that you are necessarily doing anything wrong, but it's hard to
> diagnose the potential problems without actually seeing what might be in
> those .xvg files.  Can you post short snippets of a few of them, just to
> demonstrate what the difference is?  I am wondering if there is so much
> memory required, that the calculation is dumping out the resulting data
> prematurely and therefore over-writing incomplete output files.  Just a
> guess, but worth considering.
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
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> jalemkul[at] | (540) 231-9080
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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