[gmx-users] Diagnoding + system blowing up

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jul 28 16:45:25 CEST 2012

On 28/07/2012 9:34 PM, Shima Arasteh wrote:
>   Hi all,
> My system has got BLOWING UP . I followed the protocol in http://www.gromacs.org/Documentation/Terminology/Blowing_Up and got as below:
> Step 1: If the crash is happening relatively early (within a few steps), set nstxout (or nstxtcout) to 1, capturing all possible frames.  Watch the resulting trajectory to see which atoms/residues/molecules become unstable first.
> I got this warning:
> Warning: 1-4 interaction between 5 and 18 at distance 2.003 which is larger than the 1-4 table size 2.000 nm

Classic symptom of blowing up, and much more so than all of the other 
problems you reported. Please get in the habit of reading all the output 
before reaching conclusions ;-)

> Step 2: Simplify the problem:
> If you have a new box of solvent, try minimizing and simulating a single molecule to see if the instability is due to some inherent problem with the  molecule's topology or if instead there are clashes in your starting configuration.
> I got this:
> Now there are 24 residues with 360 atoms
> Making bonds...
> Warning: Long Bond (1-18 = 0.357049 nm)

So you were ignoring warnings from pdb2gmx...? There's a lesson there - 
everything you've done after ignoring that was doomed to fail. It can be 
right to ignore a warning, but you should know why it is right. If your 
topology defines a bond between atoms that are 0.35nm apart in your 
starting configuration, then either your topology or configuration have 
a serious problem.

So satisfy yourself whether there should be such a bond in the topology, 
or whether the starting geometry is silly.

> Step 3: Monitor various components of the system's energy using g_energy.  If an intramolecular term is spiking, that may indicate improper bonded parameters, for example.
> The improper-dihedral plot is strange. It "goes up in first picoseconds" and then goes down slightly.

Sure, you probably have some inappropriate bond interaction, so 
something has to give. The thing that looks weird is not necessarily the 
cause of the problem, though...

> I think there is something wrong in dihedrals which I defined in .rtp file in the new residue. atom 18 is the H atom of formyl ( Formyl is as the N-terminus and  is connected to a Valine residue)

And atom 1 or 5 is...? Does that make sense?


> Now , what do I need to do? Going to the next step of diagnosing? or no? How can I fix the problem?
> Would you mind helping me please and give me suggestions?
> Thanks in advance.
> Sincerely,
> Shima

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