[gmx-users] Lincs warning in free energy calculation

[Sadaf Rani]

Dear Gromacs users
I ran an MD simulation for 3ns and from the last coordinates started a free
energy calculation for 3ns. My system is well equilibrated but after 710725
steps I am getting Lincs warning every time as below:-

WARNING: There are no atom pairs for dispersion correction
starting mdrun 'GROtesk MACabre and Sinister in water'
1500000 steps,   3000.0 ps.

Step 710726, time 1421.45 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000003, max 0.000023 (between atoms 5470 and 5472)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   43.8    0.1080   0.1080      0.1080

Step 710726, time 1421.45 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000003, max 0.000021 (between atoms 5470 and 5472)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3437   3438   43.1    0.1080   0.1080      0.1080

I have added restraints between atoms of ligand and protein and getting
Lincs warning between 1 atom included in restraints as below:-

[ bonds ]
;    i     j  type     r0A     r1A     r2A    fcA    r0B     r1B     r2B
 fcB
  *3437*  7908    10     0.418   0.418   10.0   0.0    0.418   0.418   10.0
  41840.00

[ angle_restraints ]
;   ai    aj    ak    al  type    thA      fcA    multA  thB      fcB
 multB
  3437  7908  7906  7908       1    100.29   0.0    1     100.29   418.40
1
  7908  3437  3439  *3437*       1    146.50   0.0    1     146.50   418.40
  1

[ dihedral_restraints ]
;   ai    aj    ak    al   type    phiA     dphiA  fcA    phiB      dphiB
 fcB
  7906  7908  *3437*  3439     1    156.16   0.0    0.0    156.16    0.0
 418.40
  7907  7906  7908  *3437*     1    -56.93   0.0    0.0    -56.93    0.0
 418.40
  7909  *3437*  3430  3435     1    131.32   0.0    0.0    131.32     0.0
418.40

Can anyone please suggest to me how Should I fix this error? Any help will
be really appreciated.

Thanks.

Sadaf