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
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
