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

[Sarah Witzke]

Hi Tsjerk and others,
 
This is a very good explanation! Thank you. Did you mean I should file a bug report or are you doing it since you understand the code?
 
Thank you all!
Sarah 

________________________________

Fra: gmx-users-bounces at gromacs.org på vegne af Tsjerk Wassenaar
Sendt: on 02-12-2009 19:29
Til: jalemkul at vt.edu; Discussion list for GROMACS users
Emne: Re: SV: SV: SV: [gmx-users] g_saltbr



Hi,

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

  if (bSep) {
    snew(buf,256);
    for(i=0; (i<ncg); i++)
      for(j=i+1; (j<ncg); j++) {
        if (nWithin[i][j]) {
          sprintf(buf,"sb-%s:%s.xvg",cg[i].label,cg[j].label);
          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:

      sprintf(buf,"%s%d",*(atoms->resname[resnr]),resnr+1);
      cg[ncg].label=strdup(buf);

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...

Cheers,

Tsjerk

On Wed, Dec 2, 2009 at 7:10 PM, Justin A. Lemkul <jalemkul at vt.edu> 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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



--
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php