<br>Yegor, Yegor, Yegor,<br><br>Though maybe not the most intuitive software around, Gromacs serves many people on the globe in their attempts to understand the world around by looking at the computed wiggling, bumping and such of atoms in all kinds of systems. If it's a barely useful package, that can only be true from your frame of reference, which, beyond doubt, is shared my the majority of humanity, since these are more interested in playing Quake or other games than they are in solving biological or physics puzzles.
<br><br>If you are interested in doing MD, you have plenty of choices. NAMD, CHARMM, AMBER, GROMOS, GROMACS, and many more. We by no means intend to force you in using GROMACS. If it isn't what you expect from an MD package.., try another one. But do expect that each of these packages requires understanding of the principles of molecular simulations and takes a good deal of effort to get the things you want to have done actually done.
<br><br>Besides, just because you fail on a saturday afternoon to get a linker modeled in gromacs and run your simulation with it, doesn't make the package useless. Most people can live without that linker and just want 'normal' proteins. Before adding such a linker, you require much more knowledge about the package your using, with regards to topologies, force fields, etc, etc. I understand your frustration with your attempts to get it done, as I've been there before, but it won't be anything different for any of the other packages. We're not doing magic here.
<br><br>I'll try to summarize the last two paragraphs to interpret them from your reference frame:<br>All molecular dynamics packages are barely useful. <br><br>If you are serious about doing MD, then try your best in understanding your problem. Try hard to work out a solution and if you run into a problem with your suggested solution, ask (without aiming your frustration to the developers or the users of the list). Remember that all of us are trying to do what no one has boldly done before, and therefore we'll all encounter (have encountered) these roadblocks in one way or another.
<br><br>Tsjerk <br><br><div><span class="gmail_quote">On 2/23/06, <b class="gmail_sendername">Yegor Isakov</b> <<a href="mailto:gromacs_problems@yahoo.com">gromacs_problems@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
That is not about any kind of etiquette. Despite enormous efforts of those developers the package is barely usefull, that is it.</blockquote></div><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>