[gmx-users] minimization and simulation problems

[chris.neale at utoronto.ca]

What are your initial box dimensions prior to em? Also, please copy  
and paste your .mdp options. Also, what happens when you run the same  
post-em simulation with nsteps=1 ?

-- original message --


Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
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_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

-------------------------------------------------------

"It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348

Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.

-------------------------------------------------------
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2[cli_2]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2

gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1[cli_1]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1

When I looked at the pdb file attached I see something strange that is
happening at the edges of the box.
I can't understand what is the problem. Can someone help me with it?
Thank you in advance.
Regina

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