Try adding "lincs-order = 6" to your mdp file. The following settings don't give me lincs warnings at 500 K, though I presume that the lincs-order is the essential part.
constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs dt = 0.002 integrator = sd tc_grps = System tau_t = 1.0 ld_seed = -1 failing that, post your full .mdp file. ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sidong Tu <sido...@g.clemson.edu> Sent: 09 August 2016 14:49:03 To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: Chandan K Choudhury Subject: [gmx-users] LINCS warnings at high temperature md run Dear all, I was trying to simulate lysozyme and polymer in water model tip3p using charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU and the system size was about 60,000 atoms. I have done equilibrium with Berendsen(B) and Parrinello-Rahman(PR), and then md. The thermal coupling I used was v-rescale. I always got a LINCS warning and my job stopped during the md. Here's the parameter I have used: Stage Position_Constraint Pcoupl gen_vel LINCS dt nsteps 1 Protein & polymer B yes all bonds 0.002 200,000 2 Protein B yes all bonds 0.002 200,000 3 None B yes all bonds 0.002 200,000 4 None PR no all bonds 0.002 50,000 5 None PR no h bonds 0.002 1.25e+8 At stage 5, the md run stopped at 149 steps and showed relative constraint deviation after LINCS. I have searched for this warning and there is an explanation that it might be introduced by the bad equilibrium. Then I added a equilibrium stage with Berendsen pressure coupling after stage 3 with LINCS constraints of h bonds for 50,000 steps without position constraints. This time there was still warings with LINCS and it stopped at step 79026 in md: Step 79026, time 158.052 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 15.598468, max 1553.834961 (between atoms 15966 and 15968) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 15941 15943 40.7 0.2082 0.1109 0.1111 15945 15946 75.6 0.2551 7.7014 0.1111 15945 15947 90.0 0.2299 4.2042 0.1111 15949 15950 67.8 0.1543 0.1150 0.1111 15949 15951 86.2 0.1658 8.9758 0.1111 15966 15967 90.0 0.1111 0.2587 0.1111 15966 15968 143.1 0.1111 172.7422 0.1111 15970 15971 90.0 0.1111 0.1405 0.1111 Wrote pdb files with previous and current coordinates The simulation worked well with dt=0.001 without LINCS. But I still want to find if there is a way to simulate at high temperature(500K) with dt=0.002 so that I can use less steps? -- Sidong Tu Department of Materials Science and Engineering Clemson University Phone: (213)265-6768 -- 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.