[gmx-users] help

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 27 19:47:32 CEST 2010

Lucio Ricardo Montero Valenzuela wrote:
> hello. I got the same error, because I was using an NPT ensemble to do a
> position-restrained simulation, and the error disappeared when I did the
> position-restrained simulation with NVT.

I would be careful about ad hoc changes to the statistical mechanical ensemble 
to try to circumvent a problem like this one.  The answer to these types of 
errors is always the same: the model physics has broken, causing the system to 
explode.  There are several reasons for this to occur, and in your case, perhaps 
your system simply wasn't "ready" for pressure coupling :)

The original poster has provided insufficient information about the system to 
provide anything beyond speculation as to how to fix this problem.


> Best regards.
> Lucio.
> El mar, 27-04-2010 a las 16:52 +0530, vani ms escribió:
>> hello 
>> i got the warning as the Warning: "1-4 interaction between 246 and 251
>> at distance 4.991 which is larger than the 1-4 table size 2.400 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
>> or 
>> with user tables increase the table size
>> Segmentation fault"
>> so tl me wt actually is table extension and table size in mdp file
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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