[gmx-users] Sorry

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 31 22:28:38 CET 2008

Chih-Ying Lin wrote:
> Hi Tsjerk and all Gromacs contributors:
> I am very sorry about my inappropriate ways of asking questions.
> I am really totally new in Gromacs, MD,  Linux, C programmings, and Bio-tech.
> No one can discuss with me locally so the thing I can do is to post
> all my questions on the mailing lists. Before this, I did read through
> all of the manual. Obviously, I did not fully understand what the
> manual told me. Also, I made efforts "try and error ".
> I was assigned a system, in which the HOME-MADE molecules is arround
> water. They will aggregate and form micelles.
> So, I made the .gro and the .top manually; then it have problems later
> on when I add water and ions on my system.

This is a bad project to give someone for their first experience at MDS, 
especially if they lack a local "expert" to teach them anything. There 
are hugely many pitfalls and lots of people fall into them because they 
try to run too quickly.

Crafting a topology for an arbitrary molecule is tricky, as you've seen.

I'd strongly suggest you experiment first with a micelle aggregation 
system for which you can use someone else's trustworthy topology (maybe 
from some tutorial?). That way you can learn how to operate the 
simulation without being distracted by whether (or when!) things are 
breaking in your topology.

Do keep reading the manual - it's really a very good reference.


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