Dear Justin, I am so thankful for you kindly reply. Now, I can solve this problem.
Tuong Vy On Tue, Oct 6, 2015 at 11:49 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/6/15 3:26 AM, Vy Phan wrote: > >> Dear all gromacs Users! >> I want to run a simulation with the system protein-ligand (I have several >> ligands). >> With EM, nvt, npt step I put position restraint for the ligands and all >> thing was fine. After that, I run production simulation without position >> restraint of ligands. I saw the ligand move out of the initial position >> and >> simulation was stopped. >> >> Did the LINCS warning happen because this system is not stable ? >> > > Yes. > > How can I keep the continuous running simulation without the LINCS >> warnings? I want the ligands are free to move and find their binding >> sites. >> >> > Either your ligand topology is not stable or your run settings are not > sensible. Please see any of the million or so posts in the gmx-users > mailing list archive regarding similar or identical situations. > > -Justin > > This is the warnings: >> 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 >> >> Thank you so much for any suggestions >> Tuong Vy >> >> > -- > ================================================== > > 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.
