[gmx-users] Diagnoding + system blowing up

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Jul 28 13:34:41 CEST 2012

 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

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)

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?

Would you mind helping me please and give me suggestions?

Thanks in advance.


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