[gmx-users] Problems with FENE potential

[Marisa Roman]

Hi there,
I have been trying to run a simulation using the fene potential option in a chain of beads as model for my protein, ubiquitin and the sd integrator.
The problem comes when one of the beads goes beyond the limits and comes out from the other side of the box, the distance comes out taking into account the position on the other side of the box and not the real one. Therefore my system collapses.
Any suggestion on this will be very appreciated.

Marisa Roman
Philadelphia, US

PS: I could print out coordinates of the beads involved to see the problem:

step 970, will finish at Wed Oct  7 13:42:36 2009BONDS: x[42] = (3.533585 2.817612 14.356295 ); x[43] = (3.469475 2.807785 14.618975 )  dr2= 0.0732075 
BONDS: x[42] = (3.533310 2.820071 14.356031 ); x[43] = (3.467908 2.807405 14.620831 )  dr2= 0.0745564 
BONDS: x[42] = (3.532996 2.822756 14.356280 ); x[43] = (3.466114 2.806527 14.622769 )  dr2= 0.0757529 
BONDS: x[42] = (3.532656 2.825698 14.357033 ); x[43] = (3.464116 2.805169 14.624761 )  dr2= 0.0767974 
BONDS: x[42] = (3.532295 2.828872 14.358303 ); x[43] = (3.461922 2.803345 14.626786 )  dr2= 0.0776872 
BONDS: x[42] = (3.531900 2.832249 14.360102 ); x[43] = (3.459582 2.801082 14.628803 )  dr2= 0.0784018 
BONDS: x[42] = (3.531463 2.835809 14.362425 ); x[43] = (3.457096 2.798412 14.630804 )  dr2= 0.0789566 
BONDS: x[42] = (3.530972 2.839528 14.365273 ); x[43] = (3.454516 2.795343 14.632739 )  dr2= 0.0793356 
BONDS: x[42] = (3.530426 2.843364 14.368648 ); x[43] = (3.451869 2.791898 14.634576 )  dr2= 0.0795378 
BONDS: x[42] = (3.529795 2.847286 14.372531 ); x[43] = (3.449184 11.288118 14.636299 )  dr2=   71.3237 

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Program mdrun, VERSION 4.0.5
Source code file: bondfree.c, line: 325

Fatal error:
 x[42] = (3.529795 2.847286 14.372531 ); x[43] = (3.449184 11.288118 14.636299 );
 r^2 (71.323738) >= bm^2 (0.324900) in FENE bond between atoms 43 and 44
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