[gmx-users] Box Exploding Error

[VENKATESH HARIHARAN]

I would like to thank everyone for their help.  Several individuals responded
to my initial post.
The consensus seemed to be to use distance restraints.  My question is, because
distance restraints
creates penalties if the distance between two atoms EXCEEDS UPPER BOUNDS,
wouldn't that apply more for pulling
two terminal atoms apart? In example, as the peptide is being pulled apart, if
the distance exceeded a certain
value, a penalty would be assessed to the force.  In my simulation, with the
terminal ends coming together, how
UPPER bounds be set?  Would I set my upper bounds very low (i.e. - 0.5 nm
range)?  This way, even the starting
structure, with the distance between the terminal ends starting at ~3.5 nm,
would be assessed a penalty.  Another
idea suggested by the GROMACS manual was to incorporate a [bonds] type 6
exclusion in the topology, to create a
harmonic potential between the two atoms.  Would this serve to help bring the
two ends together during simulation?
Again, much thanks to those who responded.

--Venk


VENKATESH HARIHARAN wrote:
>> Hello All,
>> 
>> First, for this question I am referring to GROMACS 3.3.3.  I have 
>> thoroughly read the archives for errors on why a simulation box might 
>> explode.  My simulations require that I bring the N and C terminal ends 
>> of a ~20 amino acid peptide as close together as possible.  To do this, 
>> I am using the pull code to freeze the C terminus and pull the N 
>> Terminus toward it.

>I would use normal MD with distance restraints between suitable terminal 
>atoms. This is a much simpler approach to this problem.

>>  I keep getting the following error during the 
>> simulation:
>> 
>> Back Off! I just backed up md_traj.xtc to ./#md_traj.xtc.1#
>> Warning: 1-4 interaction between 5 and 10 at distance 1.480 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

>See <a target="_new"
href="http://wiki.gromacs.org/index.php/blowing_up">http://wiki.gromacs.org/index.php/blowing_up</a>

>> My question: Is there any way to completely ignore this error, so that 
>> the N Terminus is pulled as close as possible to the C Terminus?

>That's not your problem. Atoms 5 and 10 are too close because there's 
>something unphysical about your model, and anyway these atoms are not 
>your terminal pair.

>>  I 
>> understand that the results in the .pdo file of the pull simulation may 
>> be unrealistic, but I simply need to get a peptide structure whose N and 
>> C Terminal ends are close together (within .5 nm).  On a side note, are 
>> there any suggestions for respectable molecular modeling software with 
>> which I may be able to BUILD a circular peptide (i.e. - N and C Terminal 
>> ends are brought close together)?  Any help is appreciated.

>There are a few links here 
><a target="_new" href="http://wiki.gromacs.org/index.php/Coordinate_File">http://wiki.gromacs.org/index.php/Coordinate_File</a> that might help.

>Mark
______________________________

Venkatesh Hariharan
The Pennsylvania State University
Schreyer Honors College
Undergraduate - Bioengineering

"You must be the change you wish to see in the world."
--Mohandas Karamchand Gandhi


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