[gmx-users] about "LINCS WARNING"

[Kun-Lin Yang]

Hi there:

        I happened to simulate a similar problem with decanol and water interface, and I don't have any problems with mdrun.   I guess you have to check your initial configuration (to see if there is any overlap or unwanted contact) rather than the parameters in em.mdp.  The parameters there come with GROMACS are just fine.  BTW, I noticed that you erased a line, define = -DFLEX_SPC, which may cause trouble too.  

Kun-Lin, 1/13


  Dear Sir or Madam:

       I am trying to simulate the interface between alkyls & water, the decane (C10 , declared in ffgmx.itp) and SOL (OPLS) are used. 

  But I've met some problems:

  1. mdrun always throw some error message, then stoped

  2. how to enlarge "energy minimize " step length? I'd modified the "emstep ", but the mdrun shinked it rapidly.

   

  Could you please give me some advice?

  Thank you very much in advance!

   

  rayn

   

  Step 0, time 0 (ps)  LINCS WARNING

  relative constraint deviation after LINCS:

  max 40.729252 (between atoms 1854 and 1855) rms 1.751049

  bonds that rotated more than 30 degrees:

   atom 1 atom 2  angle  previous, current, constraint length

      391    392   46.6    0.1530   0.1549      0.1530

      392    393   45.9    0.1530   0.1517      0.1530

      738    739   35.7    0.1530   0.1851      0.1530

      739    740   90.0    0.1530   0.1464      0.1530

     1245   1246   35.2    0.1530   0.1874      0.1530

  .....

   

   

   

  My em.mdp : 

  constraints         =  none

  integrator          =  steep

  dt                  =  0.0001  

  nsteps              =  5000         

  nstlist             =  0

  ns_type             =  grid

  rlist               =  1.0

  rcoulomb            =  1.0

  rvdw                =  1.0

  emtol               =  10.0 

  emstep              =  0.5

  nstcgsteep         =  100

   

   

   

   

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