[gmx-users] using pull code with coarse grained model
Ashish Gupta
agupta at che.ufl.edu
Thu Feb 8 06:39:56 CET 2007
Hello gmx-users,
I am trying to run constraint simulation constraining a particle at
a particular distance from the bilayer. I am using Marrink's coarse
grained model. When using the pull code when constraining the
particle I get the following error attached below. If I simply run
the tpr file without the pull code then the simulation runs fine.
So I guess there are no bad contacts in my system. I have used the
pull code before without any problems but in this case something
seems to be not working.
I will appreciate if somebody can point out how to correct my
simulations or is there a bug in the pull code.
I am using a tau_p value of 1 ps. I am also attaching the ppa file i
used. I got the same error when running it on different machines so it
seems not a hardware issue. The ppa file is attached.
The error I got is
"
Reading file EQ.tpr, VERSION 3.3 (single precision)
Loaded with Money
Back Off! I just backed up ener.edr to ./#ener.edr.6#
Reading parameter file pullout.ppa
Back Off! I just backed up pullout.ppa to ./#pullout.ppa.5#
Groups: HNP1
Reference Group: DPPC
Using 1 pull groups
Using distance components 1 1 1
Using directional constraining 0.00 1.00 0.00
Back Off! I just backed up pull.pdo to ./#pull.pdo.5#
starting mdrun '1 HNP1 and 10X10 DPPC bilayer'
1500 steps, 6.0 ps.
Back Off! I just backed up traj.trr to ./#traj.trr.5#
step 0Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
-------------------------------------------------------
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 220
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
-------------------------------------------------------
"Shaken, not Stirred" (J. Bond)
"
Regards,
Ashish Gupta
--
Ashish Gupta,
Ph.D. Candidate,
Chemical Engg.,
University of Florida,
Gainesville FL 32611
Ph- 352-328-7335
GO GATORS!
2006 National Basketball AND Football Champions
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