[gmx-users] Diagnoding + system blowing up

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Jul 28 15:01:56 CEST 2012

I thought that the problem is with atom 18. 
Allright, I'll go through the protocol again . 

Thanks Justin.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, July 28, 2012 5:25 PM
Subject: Re: [gmx-users] Diagnoding + system blowing up

On 7/28/12 7:34 AM, 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

The output shown has nothing to do with the suggested diagnostic step.  At what 
time step does this occur?  Have you done what "Step 1" suggests, and if so, 
have you watched the resulting trajectory to see what happens?

> 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)

Again this output is not really relevant to the suggested "Step 2" - this is 
from pdb2gmx.  What are atoms 1 and 18?  It seems that the starting geometry is 
very poor.  Long bonds indicate missing residues or atoms or just a bad 

> 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.
> 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)
> Now , what do I need to do? Going to the next step of diagnosing? or no? How can I fix the problem?

I think you need to back up and do some relevant investigating in steps 1 and 2 
first.  You haven't really followed any of the advice given thus far so you're 
sort of shooting in the dark.  Something is clearly wrong either in the topology 
or the starting configuration, but it is not apparent at this point which it is.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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