[gmx-users] Lincs warning in free energy calculation

[FAISAL NABI]

Check the forcefield you are using is appropriate for your system or  there
might be some problem with the ligand parameters.

On Tue, Mar 24, 2020 at 11:30 AM Sadaf Rani <sadafrani6 at gmail.com> wrote:

> 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
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-- 

Faisal Nabi

*Pre-Doctoral Fellow (CSIR-JRF)*
C/o Professor Rizwan Hassan Khan
Interdisciplinary Biotechnology Unit,
Aligarh Muslim University, Aligarh, UP, INDIA.
Email-            *fnabi at myamy.ac.in <fnabi at myamy.ac.in>*
*                      faisalbiochem at gmail.com <faisalbiochem at gmail.com>*
Contact no. - *+91-8923713214*