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.
