Hi, It seems likely that you've changed something before this restart, which may not have been a good idea. What did you actually do?
Mark On Mon, 11 Apr 2016 08:11 Sarath Chandra <sarathchandrada...@gmail.com> wrote: > You should re-run your simulation writing out the xtc file more frequently > to check which part of the protein/ligand is having structural issues > (considering that your mdp and other settings are accurate). Also run a > g_energy to check if the energy terms are doing fine. LINCS is pointing out > that something bad is going around the neighborhood of atoms 2835 and 2836. > Check the trajectory file in vmd/pymol to confirm that nothing is wrong > with the structures. > > As pointed out in this link > http://www.gromacs.org/Documentation/Terminology/Blowing_Up systemic > checks > of the system, forcefield parameters, and the mdp settings will present you > with the solution of this problem. > > Regards, > > Sarath > > -- > Sarath Chandra Dantu, PhD, ELS > Room No. 606, New BSBE Building > Department of Biosciences and Bioengineering > Indian Institute of Technology Bombay > Powai Mumbai, 400-076, India > > > On 11 April 2016 at 11:31, f vazifeshenas <fahim.vazifeshe...@gmail.com> > wrote: > > > 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. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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