[gmx-users] Pull Error message

Jonathan KHAO jkhao at ifr88.cnrs-mrs.fr
Tue Mar 15 23:43:57 CET 2011


I'm running MD on a 30x30x7,5nm system in which I pull two proteins  
away from each other. I have successfully pulled them apart to 9.4nm.  
But when I now use a
pull_init1      = 9.59
pull_start      = no
pull_rate1      = 0
pull_dim = Y Y Y
At one point, I get the following error message :
Distance of pull group 1 (3.637819 nm) is larger than 0.49 times the  
box size (13.774273).

The mdlib/pull.c code (l 329) shows that the 13.77423 value is ~ the  
squared value of half the smallest box vector ( wouldn't it be clearer  
to add a sqrt ?).

So I don't understand why I get the error message, especially now. If  
maximum distance is the shortest box vector, I wouldn't have been able  
to pull it to 9.59nm. And if each dimensions are treated separately, I  
should not get this error as the Z component of the distance is less  
than 1nm.

Any suggestions ?

Thanks !


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