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