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[Sunil Thapa]

Respectable Mark/Berk/David
I am trying to study diffusion of oxygen in water at a constant pressure of 1 bar. 

My system contains 2 oxygen molecules in 110 water molecules of the box size 1.5 nm
I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run mdp file.
 
When I run the production run of 1 ns then I get an warning message as follows and the run terminates. Please try to figure out what might have been wrong.
 
Grid: 35 x 35 x 35 cells
WARNING: your box is exploding! (ncells = 42875)
           Step           Time         Lambda
          17200       34.40000        0.00000
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         1.000000      1      2   1.000000
        After LINCS         1.000000      1      2   1.000000
Fatal error: Can not read/write topologies to file type unknown
 
 
If I change the LINCS to SHAKE with tau_p=0.5 it goes well but at the last step it gives segmentation fault error. I checked the pdb after energy minimization. The molecules are intact and the energy is well converged.
If I increase tau_p=2.0, also at this step the error persists.
My system contains 2 oxygen molecules in 110 water molecules of the box size 1.5 nm
I have set rvdw=0.7/0.5, rcoul=0.7/0.5 and rlist=0.7/0.5 in my main run mdp file. 
 
Your help is a boon
Sunil



      
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