[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broke

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
>>From Tsjerk,
> "Previously you had an issue with the addition of ions to your .top
> file. In your protocol, it's not mentioned. Have you made sure that
> issue is cleared?"   => Yes, I did.
> 
> 
> 
> I encountered two cases that my simulation broke.
> Case I => 6LYZ + ligands + water molecules + CL-
>            => Gromacs 3.3.3
>            => error from the addition of ions to my .top file
>            => The problem is solved and the simulation runs successfully.
> 
> 
> Case II => 6LYZ + water molecules + CL-
>             => Gromacs 4.0.5
>             => Have tried the correct addition of ions to my .top file
>             => The potential energy goes very negative after EM
>             => the PR step broke.

Almost certainly, you've done it wrong. I've lost track of how many 
times you've posted this little detail about what you've done. We're not 
at all interested in seeing just a broad description of what you've 
done. The details all have to be right, and since you have a problem 
with a relatively simple stage of doing MD, you're getting at least one 
detail wrong. Accordingly, we're not much interested in anything that's 
been filtered through your head, because we all know our heads are 
imperfect and computers are literal.

Start from a clean working directory and produce an actual list of 
commands you've used, by copying and pasting from your terminal. I've 
given you that kind of advice at least three times now. If you want 
people to help, please look like you're trying to follow their advice. 
We don't owe it to you. If you want help, you need to make it easy for 
us to help you.

Mark