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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 11 12:38:05 CET 2010

Hi Chih-Ying,

Like Mark said, start from scratch and trace your steps carefully.
There's nothing special about that lysozyme structure. In fact, the
protocols I use for the tutorials work flawlessly with it! I think
you'd best step through the tutorial again, using 6LYZ.pdb. I know
that at some points the tutorial deviates from what you need/want. In
these cases, make notes of what happens with the tutorial way of doing
it and see how your way of doing deviates from that. I'd say it's best
to change the protocol starting from the end, like changing the .mdp
options first and see whether it still goes. One of the differences
between your protocol and the one in the tutorial is likely to be the
cause of your problem. It's up to you to track it.



On Mon, Jan 11, 2010 at 10:19 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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