Dear all,<br><br>I am trying to simulate a GB simulation of a 112 amino acid long protein. I keep getting these errors,<br><br>Step 27718, time 55.436 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 33.319842, max 438.763717 (between atoms 79 and 81)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br><br>Step 27718, time 55.436 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.058237, max 1.390675 (between atoms 91 and 93)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 91 92 50.2 0.1016 0.1065 0.1010<br> 91 93 90.0 0.1002 0.2415 0.1010<br> 91 94 70.2 0.1025 0.1066 0.1010<br>
79 80 90.0 0.1057 1.0667 0.1090<br> 79 81 90.0 1.3066 47.9342 0.1090<br> 85 86 90.0 0.1084 0.1758 0.1090<br> 85 87 90.0 1.0654 0.1668 0.1090<br>
88 89 90.0 0.1097 0.6994 0.1090<br> 88 90 90.0 0.1125 0.1097 0.1090<br> 91 92 50.2 0.1016 0.1065 0.1010<br> 91 93 90.0 0.1002 0.2415 0.1010<br>
91 94 70.2 0.1025 0.1066 0.1010<br><br clear="all"><br>I am copying my mdp parameters below, I'd appreciate any suggestions to fix that.<br><br>integrator = sd<br>tinit = 0<br>
dt = 0.002<br>nsteps = 2500000<br>simulation_part = 1<br>init_step = 1<br><br>nstxout = 5000<br>nstvout = 5000<br>nstenergy = 500<br>
nstxtcout = 500<br>nstlog = 500<br><br>xtc_grps = System<br>energygrps = System<br>comm_mode = Linear<br>; neighbor searching and vdw/pme setting up<br>
nstlist = 10<br>ns_type = grid<br>pbc = xyz<br>rlist = 2.0<br><br>implicit_solvent = GBSA<br>gb_algorithm = OBC<br>gb_saltconc = 0.15<br>
rgbradii = 2.0<br><br>coulombtype = Cut-off<br>fourierspacing = 0.1<br>pme_order = 6<br>rcoulomb = 2.0<br><br>vdwtype = Cut-off<br>rvdw_switch = 1.0<br>
rvdw = 2.0<br><br>; cpt control<br>tcoupl = V-rescale<br>tc-grps = System<br>tau_t = 0.1<br>ref_t = 300.0<br><br>Pcoupl = Berendsen<br>
pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br><br>; velocity & temperature control<br>gen_vel = yes<br>
gen_temp = 300.0<br>annealing = no<br>constraints = hbonds<br>constraint_algorithm = lincs<br>morse = no<br><br><br>Thanks,<br>-- <br>Elif Nihal Korkmaz<br>
<br>Research Assistant <br>University of Wisconsin - Biophysics <br>Member of Qiang Cui & Thomas Record Labs<br>1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: 608-265-3644<br>
Email: <a href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br><br><br>