[gmx-users] [Fwd: How simulate two peptides in a box?]

Mark Abraham mark.abraham at anu.edu.au
Tue Jul 3 04:02:55 CEST 2007

>  Hello Gromacs users:

Please don't reply to another user's question with a change of topic and
not change the subject line of your email. Not doing this means the people
who might know the answer for you have no idea in advance what you're
going to be asking, and might not bother reading. Best is to start with a
new email, not a reply, and to use your subject line sensibly.

> I am running a  dimeric protein simulation on Gromacs 3.3 using the force
> filed G43a1.
> For initially minimizing the hydrogen i did some small minimization and
> equilibration in the vacuum by maintaining the restraints
> then i added ions and water but in the very first minimization i m getting
> the following error

If you want to keep your credibility, when people have already made a
suggestion about how to solve your problem, such as I did here
http://www.gromacs.org/pipermail/gmx-users/2007-June/028301.html, when you
post the same problem, you should say what happened when you tried their
suggestion. They didn't suggest it for their own entertainment.

Look at the minimization "trajectory" and see where things are breaking.
Have a look at your topology there, read chapter five thoroughly.


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