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

[Tsjerk Wassenaar]

Hi Sarah,

You may file the bug report. You can submit a small part of the
trajectory to reproduce the error :)

Cheers,

Tsjerk

On Wed, Dec 2, 2009 at 10:11 PM, Sarah Witzke <sawit02 at student.sdu.dk> wrote:
> 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
>>
>> ========================================
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist