[gmx-users] problem with mdrun

[poor nima]

Dear gromacs users,

 

I have to run a 1ns simulation with a protein in hexane environment. I am using a Linux system for my run. It’s a monomer protein. When I run in water I haven’t get any problem with my run. It ended successfully. But when I try to run a hexane run with the same protein it showing following error.

 

mdrun -v -s full -o full -e full -c after_full -g full >& full.job &

 

[1] 2606

 

tail -f full.job

 

 

  29959  29960   89.9  48144.9766 66764.4141      0.1530

  29960  29961   89.9  48144.5781 63069.4609      0.1530

  29961  29962   89.9  48144.9688 33113.0078      0.1530

  29963  29964   89.9  48144.9883 31983.7520      0.1530

  29964  29965   89.9  48144.8906 61253.6016      0.1530

  29965  29966   89.9  48144.9414 66282.4375      0.1530

  29966  29967   89.9  48144.8633 61631.7461      0.1530

  29967  29968   89.9  48144.7812 32032.5273      0.1530

 

Back Off! I just backed up step1.pdb to ./#step1.pdb.1#

Wrote pdb files with previous and current coordinates

 

Step 2  Warning: pressure scaling more than 1%, mu: 11704.7 11704.7 11704.7

Warning: Only triclinic boxes with the first vector parallel to the x-axis and t

he 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 t

he 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 t

he 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 t

he 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 t

he 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 t

he 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 t

he 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.

Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]

 

[1]+  Exit 255           mdrun -v -s full -o full -e full -c after_fu

ll -g full 1>&full.job

 

 




G. POORNIMA, 
Studentship Trainee, 
Bioinformatics Center,
School of biotechnology,
Madurai Kamaraj University,
Madurai. 
E.MAIL: poornings at yahoo.co.in. 


		
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