[gmx-users] Proble while running minimization using .tpr file

Xavier Periole X.Periole at rug.nl
Sat Jan 12 11:47:14 CET 2008

On Sat, 12 Jan 2008 15:04:40 +0530 (IST)
  kinshuk at chem.iitb.ac.in wrote:
> Hi All,
> Myself Kinshuk from IIT-Bombay.I have gone through gromacs mailing list
> there i came to know about you while searching the solution of the problem
> while running minimization using .tpr in position restraints steps of MD
> run.I have been performing simulation of guanidium ion & phosphate ion by
> gromacs.
> i hope i will be getting answer of my problem .
> In my case no problem is coming while running the grompp, no warning is
> coming. i could able to generate .tpr file without any error.
> problem cames only while running the minimization using the .tpr file
>For convenience, as mention earlier, following was the problem :
> ...................
> #Warning: 1-4 interaction between 1 and 9 at distance 8.443 which is larger
> than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file#

The message gives you two possible solutions:
1) your system is exploding: which suggests that the starting structure
is somehow unrealistic and the minimization is not able to fix it. Check
you starting configuration, atoms 1 and 9 ...
2) increase the size of the table in the mdp file to be able to describe
the distances up to 8.443 nm. The way to do this is certainly described
in the manual. However this is a very large distance and the case 1) is
probably what is happening.


> I will be thankful if i'll be getting solution of this problem.
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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

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