[gmx-users] About Usage of Constraints

[vidhya sankar]

Dear justin Thank you for your previous reply
                                                                        I  am running NPT Equlibration  at 20 ps  with dt 0.0002 in 100000 steps  Without usage of  Lincs Algorithm and its related parameters it runs Successfully .
But When I  Increase dt from 0.0002 to 0.002 then I have got error as follows in grompp

WARNING 1 [file 2KDQTR.top, line 71]:
  The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
  an estimated oscillational period of 1.0e-02 ps, which is less than 5
  times the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Then I have used the Lincs Algorithm and its related parameter Then I have got Error during Mdrun as follows I  saw  there Are Plenty Of discussion in Mailing list   But  I am Not Able to come to conclusion


relative constraint deviation after LINCS:
rms 0.015272, max 0.577865 (between atoms 120 and 122)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
Wrote pdb files with previous and current coordinates

   129    131   39.1    0.1475   0.1664      0.1330
    129    130   37.8    0.1191   0.1243      0.1230
    125    126   38.5    0.1738   0.1508      0.1530
    124    129  103.2    0.0962   0.9157      0.1530
    124    125  124.3    0.1725   0.8648      0.1530
    122    124  169.9    0.4717   2.5621      0.1470
    122    123  168.0    0.2655   3.1890      0.1000
    120    122  176.3    0.5957   7.3414      0.1330
    120    121  172.8    0.5550   6.4843      0.1230
What does the Above Fact Indicates I mean the Problem is in Topology or in MD Parameter file ? 

With Regards 

S.Vidhyasankar