[gmx-users] Regarding mdrun segmentation fault in cluster

[naga raju]

Dear gmx users,
                I am using mdrun command in pentium-4
redhat linux, job was completed without any errors.
When I use the same files in cluster(redhat
enterprizes OS), I got the following error, 

Grid: 14 x 14 x 15 cells
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.
                                                      
                                                      
                
                                                      
                                                      
                
   Rel. Constraint Deviation:  Max    between atoms   
 RMS
       Before LINCS         inf   6056   6059   nan
        After LINCS         inf      1      4   nan
                                                      
                                                      
                
                                                      
                                                      
                
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 1 and 4) rms nan
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint
length
      1      4   90.0    0.1470      inf      0.1470
      2      4   90.0    0.1470      inf      0.1470
      3      4   90.0    0.1470      inf      0.1470
      4      5   90.0    0.1470      inf      0.1470
      ..............................................
      ..............................................
     

 after few lines it is coming as sigmentation fault.

 I used grompp command to prepare mdrun input file
(*.tpr) in petium-4 and in cluster, I couldn't get any
warning messages in both cases.

here is my input file:

 title = dopc
 cpp   = /lib/cpp
 integrator    =    md
 dt            =    0.002
 nsteps        =    500000
#Out put control parameters
 nstxout       =    5000
 nstvout       =    5000
 nstlog        =    5000
 nstxtcout     =    0
#neighbor searching parameters
 nstlist        =    10
 ns_type       =    grid
 pbc           =    xyz
 rlist         =    1.0
#Electrostatic and VdW parameters
 coulombtype   =    PME
 pme_order     =    4
 ewald_rtol    =    1e-5
 vdwtype       =    Cut-off
 rvdw          =    1.0
#Temperature and parameters
 tcoupl        =    berendsen
 tc_grps       =    DOP SOL
 tau_t         =    0.1 0.1
 ref_t         =    303 303
#Pressure and parameters
 pcoupl        =    berendsen
 pcoupltype    =    anisotropic
 tau_p         =      1.0   1.0   1.0   1.0  1.0  1.0
 compressibility   =  5e-5  5e-5  5e-5  0.0  0.0  0.0
 ref_p         =      1.0   1.0   1.0   1.0  1.0  1.0
#Constraints parameters
 gen_vel       =    yes
 gen_temp      =    303
 gen_seed      =    17532
 constraints   =    all-bonds
 constraint_algorithm   =   lincs
 lincs_order   =    4
 lincs_iter    =    1
 lincs_warnangle  = 30
                                                      
                                                     
Can you suggest to solve the problem. 
             Thank you in advance.
                                    with best regards,
                                      NAGARAJU
MULPURI.



       
____________________________________________________________________________________
Get the free Yahoo! toolbar and rest assured with the added security of spyware protection.
http://new.toolbar.yahoo.com/toolbar/features/norton/index.php