[gmx-users] about md simulation

[amri ta]

Dear colleagues,
I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning.
Does this mean that I have go back to the CG-EM step and use the double 
precision libs?
The md.log file reads:

Initializing LINear Constraint Solver
  number of constraints is 2365
  average number of constraints coupled to one constraint is 2.5

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.336565   691       696   0.033770
        After LINCS         0.342830    698        700   0.028042

Step -1, time -0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.858278 (between atoms 3397 and 3398) rms 0.016634
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   3395   3398   76.2    0.1341   0.0446      0.1470
   3398   3399   78.8    0.1341   0.0492      0.1470
Constraint error in algorithm Lincs at step -1
Grid: 10 x 10 x 10 cells
Configuring nonbonded kernels....
Testing x86_64 SSE supports...presents
           
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         70.089874   1537   1456   0.559021
        After LINCS         29.983810   3223   3224    0.787549

Like this, errors showed "Constraint error in algorithm Lincs at step 0, step1" and the simulation stops at step 1. Do I have to modify my md.mdp to remedy this?
Your advice is appreciated.
 Best regards,

Amrita Ghosh
National Institute of Mental Health and Neurosciences,
Bangalore-29.
India.


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