<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PostalCode"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="City"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="country-region"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="Street"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="address"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceName"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceType"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
p
{mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman";}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body lang=EN-US link=blue vlink=blue>
<div class=Section1>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Ok, then please stop asking and try to use
others you thing better ! We will enjoy your quietness.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>That is not about any kind of etiquette. Despite enormous efforts of those
developers the package is barely usefull, that is it.<br>
<br>
<b><i><span style='font-weight:bold;font-style:italic'>Daan van Aalten
<vdava@davapc1.bioch.dundee.ac.uk></span></i></b> wrote:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
Dear Daniela<br>
<br>
Sorry, but I have to agree with Mark Abraham here.<br>
<br>
Although I haven't done much useful development myself apart from perhaps<br>
PRODRG, the tone of some of the questions asked absolutely amazes me.<br>
There seems to be no respect for the huge amount of work developers put<br>
into a package like Gromacs - new people come in and "just expect it to<br>
work" and if it doesn't then of course it's not their fault but that of<br>
the developers. Gromacs is *free* and the developers have no formal<br>
obligation whatsoever to help you in any way. I am sure everyone<br>
involved with Gromacs is keen to continually improve the code and would<br>
like to here about problems/bugs etc - but in properly worded E-mails,<br>
giving constructive feedback, not some kind of shouting match.<br>
<br>
I normally think that E-mails like that of Yegor Isakov don't even deserve<br>
a response, but yours does as it is an important point of dicussion.<br>
<br>
Daan<br>
<br>
<br>
On Thu, 23 Feb 2006, Daniela S. Mueller wrote:<br>
<br>
> hi,<br>
><br>
> On Thu, 2006-02-23 at 12:42 +1100, Mark Abraham wrote:<br>
> > Yegor Isakov wrote:<br>
> ><br>
> > You are much more likely to get a helpful response from the people
who<br>
> > know this software best (the programmers, who do read this list) if
you<br>
> > express a little less of your frustration, and imply less
condemnation<br>
> > of their software design choices, which you probably don't understand<br>
> > yet anyway!<br>
> ><br>
><br>
> though it might be unpleasant or even unjustified, frustrated reactions<br>
> like these are in a way understandable.<br>
><br>
> what i find less understandable and certainly a great deal less<br>
> tolerable, is the arrogance and judgement of some users of this list<br>
> towards others.<br>
><br>
> also it would make helpful responses much likelier, if those unhelpful<br>
> responses were omitted.<br>
><br>
> regards,<br>
> daniela<br>
><br>
><br>
> > Check your assumptions - you haven't paid anybody for the right to
rant<br>
> > at them :-) You'd also do well to remember that GROMACS doesn't come<br>
> > with a warranty of fitness for any purpose :-)<br>
> ><br>
> > > I would be extremely pleased if anybody would tell me how could
I foce<br>
> > > that stupid pdb2gmx program to follow the path to the directory<br>
> > > containing .itp files (~/share/top).<br>
> ><br>
> > Setting the environment variable GMXLIB makes various GROMACS
utilities<br>
> > look there instead of the default, which is probably<br>
> > $GMXDATA/gromacs/top. GMXDATA gets set when you run GMXRC which is<br>
> > installed in the same place as the GROMACS binaries. You may need to<br>
> > link the existing contents of $GMXDATA/gromacs/top/ to ~/share/top/
in<br>
> > order to have everything work, as I couldn't get GMXLIB to accept a
path.<br>
> ><br>
> > I note that the manual mentions GMXLIB only in passing in a few of
the<br>
> > programs' man pages, and not at all in the Appendix section on<br>
> > Environment variables. Usage of GMXRC is also not mentioned in the<br>
> > installation section on the web page. Can either of both of these be<br>
> > looked at, please?<br>
> ><br>
> > > Although in the manual it was recomended to avoid modifying .rtp
files,<br>
> > > that is the only way I found to produce a topology
"semi-automatically."<br>
> > > Is there any other reasonable way to produce a topology? Is
anywhere<br>
> > > more intelegent converter of pdb files? Is anywhere a program
that<br>
> > > permits creating a stable bond between 2 atoms in a topolgy
without<br>
> > > blowing up the last one?<br>
> ><br>
> > Construction of topologies for MM calculations is a process that<br>
> > involves making judgements. Automating "sensible" defaults
is an<br>
> > extremely tricky business, given the multiplicity of force fields,
the<br>
> > kinds of kludgey PDB files that you can get hit with, and the<br>
> > innumerability of the molecules people will want to use. Then of
course,<br>
> > a default someone thinks is sensible, someone else will think is<br>
> > ludicrous, and they might both be right for different applications.<br>
> > Basically you will need to do some work yourself if you are doing<br>
> > something new... big surprise.<br>
> ><br>
> > Mark<br>
><br>
><br>
> --<br>
><br>
> Daniela S. Mueller<br>
><br>
> biologist (Diplom, German degree)<br>
> ______________________________________________________________________<br>
><br>
> - Molecular Dynamics Group, UQ -<br>
><br>
> Address:<br>
> School of Molecular and Microbial Sciences (SMMS)<br>
> <st1:place w:st="on"><st1:PlaceName w:st="on">Chemistry</st1:PlaceName> <st1:PlaceType
w:st="on">Building</st1:PlaceType></st1:place> (#68)<br>
> <st1:place w:st="on"><st1:PlaceType w:st="on">University</st1:PlaceType>
of <st1:PlaceName w:st="on">Queensland</st1:PlaceName></st1:place><br>
> Qld 4072, Brisbane<br>
> <st1:country-region w:st="on"><st1:place w:st="on">Australia</st1:place></st1:country-region><br>
><br>
> Phone: +61-7-33653732<br>
><br>
> Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm<br>
><br>
> **********************************************************************<br>
><br>
> - MD group, RuG -<br>
><br>
> Address:<br>
> Molecular Dynamics<br>
> Dept. of Biophysical Chemistry<br>
> <st1:place w:st="on"><st1:PlaceType w:st="on">University</st1:PlaceType>
of <st1:PlaceName w:st="on">Groningen</st1:PlaceName></st1:place><br>
> Nijenborgh 4<br>
> 9747 AG <st1:City w:st="on"><st1:place w:st="on">Groningen</st1:place></st1:City><br>
> The <st1:country-region w:st="on"><st1:place w:st="on">Netherlands</st1:place></st1:country-region><br>
><br>
> Website: http://www.rug.nl/gbb/md<br>
> ______________________________________________________________________<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list gmx-users@gromacs.org<br>
> http://www.gromacs.org/mailman/listinfo/gmx-users<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to gmx-users-request@gromacs.org.<br>
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>
><br>
<br>
<br>
##############################################################################<br>
Dr. Daan van Aalten Wellcome Trust Senior Fellow / Reader<br>
Wellcome Trust Biocentre, <st1:Street w:st="on"><st1:address w:st="on">Dow
Street</st1:address></st1:Street> TEL: ++ 44 1382 344979<br>
Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764<br>
<st1:place w:st="on"><st1:PlaceType w:st="on">School</st1:PlaceType> of <st1:PlaceName
w:st="on">Life Sciences E-mail</st1:PlaceName></st1:place>: see WWW page<br>
<st1:PlaceType w:st="on">Univ.</st1:PlaceType> of <st1:PlaceName w:st="on">Dundee</st1:PlaceName>,
<st1:place w:st="on"><st1:City w:st="on">Dundee</st1:City> <st1:PostalCode
w:st="on">DD1 5EH</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>
WWW: http://davapc1.bioch.dundee.ac.uk<br>
_______________________________________________<br>
gmx-users mailing list gmx-users@gromacs.org<br>
http://www.gromacs.org/mailman/listinfo/gmx-users<br>
Please don't post (un)subscribe requests to the list. Use the <br>
www interface or send it to gmx-users-request@gromacs.org.<br>
Can't post? Read http://www.gromacs.org/mailing_lists/users.php<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=1 width="100%" align=center>
</span></font></div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Yahoo! Mail<br>
<a
href="http://us.rd.yahoo.com/mail_us/taglines/pmall2/*http:/photomail.mail.yahoo.com">Use
Photomail</a> to share photos without annoying attachments.<o:p></o:p></span></font></p>
</div>
</body>
</html>