Thanks a lot for your guidance. I was trying to Run this protein with ligand for 20ns and in first 11ns of it i did get this LINCS error.
Step 5009957, time 10019.9 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000219, max 0.005436 (between atoms 2836 and 2835) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2836 2835 90.0 0.1236 0.1005 0.1000 ------------------------------ ------------------------- Program gmx, VERSION 5.0.5 Source code file: /home/soft/gromacs-5.0.5/src/gromacs/mdlib/constr.c, line: 224 Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I have read the link and it referred to system blowing up. How can i be assured that my system is blown up? and if it is it right to use "-append" in this condition? On Sun, Apr 10, 2016 at 5:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/10/16 2:48 AM, f vazifeshenas wrote: > >> Dear all >> Hi >> I am trying to Run one protein with ligand and i am getting a note and an >> error as fallows: >> >> Step 5009957, time 10019.9 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.000219, max 0.005436 (between atoms 2836 and 2835) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 2836 2835 90.0 0.1236 0.1005 0.1000 >> >> ------------------------------------------------------- >> Program gmx, VERSION 5.0.5 >> Source code file: /home/soft/gromacs-5.0.5/src/gromacs/mdlib/constr.c, >> line: 224 >> >> Fatal error: >> Too many LINCS warnings (1000) >> If you know what you are doing you can adjust the lincs warning threshold >> in your mdp file >> or set the environment variable GMX_MAXCONSTRWARN to -1, >> but normally it is better to fix the problem >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ------------------------------------------------------- >> Does anybody know to deal with this LINCS error? >> >> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- 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.
