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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
