Hi, all I use GMX4.5.5, GROMOS96 53a6 force field ro simulation 1dx0.pdb, I use two steps energy minimization (steep and cg ) in vacuum as follows:
1. pdb2gmx -f 1dx0.pdb -o xxx.gro -ignh -ter -water spce -ss -p xxx.top 2. editconf -f xxx.gro -o xxx.pdb -c -d 0.9 -bt cubic 3.grompp -f em.mdp -c xxx.pdb -p xxx.top -o xxx.tpr 4.mdrun -v -s xxx.tpr -nt 2 -deffnm em_xxx 5.grompp_d -f cg.mdp -c em_xxx.gro -p xxx.top -o xxx.tpr 6.mdrun_d -v -s xxx.tpr -nt 2 -deffnm cg_xxx steep is no problem, while cg have some warnings: Step 143, Epot=-1.190781e+04, Fnorm=3.680e+01, Fmax=7.027e+02 (atom 217) Step 144, Epot=-1.190936e+04, Fnorm=2.620e+01, Fmax=2.688e+02 (atom 217) Step 145, Epot=-1.191034e+04, Fnorm=2.618e+01, Fmax=2.276e+02 (atom 277) Step 146, Epot=-1.191235e+04, Fnorm=3.672e+01, Fmax=4.235e+02 (atom 277) Step 147, Epot=-1.192020e+04, Fnorm=6.482e+01, Fmax=8.288e+02 (atom 219) Step 148, Epot=-1.196346e+04, Fnorm=1.315e+02, Fmax=1.971e+03 (atom 378) Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000694, max 0.004189 (between atoms 296 and 297) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.009008, max 0.056534 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 181 182 31.3 0.1000 0.1000 0.1000 685 688 37.8 0.1000 0.1051 0.1000 262 263 41.0 0.1000 0.1000 0.1000 1 4 39.2 0.1000 0.1057 0.1000 Step 149, Epot=-1.197948e+04, Fnorm=1.069e+02, Fmax=1.271e+03 (atom 218) Step 150, Epot=-1.198617e+04, Fnorm=6.868e+01, Fmax=9.492e+02 (atom 218) Step 151, Epot=-1.199312e+04, Fnorm=6.069e+01, Fmax=8.678e+02 (atom 378) Step 152, Epot=-1.199645e+04, Fnorm=2.884e+01, Fmax=3.323e+02 (atom 378) Step 153, Epot=-1.199771e+04, Fnorm=2.482e+01, Fmax=2.873e+02 (atom 378) Step 154, Epot=-1.199942e+04, Fnorm=3.681e+01, Fmax=6.652e+02 (atom 378) Step 155, Epot=-1.200439e+04, Fnorm=7.122e+01, Fmax=1.091e+03 (atom 378) . . . . . Step 208, Epot=-1.231153e+04, Fnorm=2.409e+01, Fmax=2.882e+02 (atom 262) Step 209, Epot=-1.231272e+04, Fnorm=2.635e+01, Fmax=3.012e+02 (atom 261) Step 210, Epot=-1.231523e+04, Fnorm=3.957e+01, Fmax=7.031e+02 (atom 378) Step 211, Epot=-1.232519e+04, Fnorm=6.187e+01, Fmax=1.273e+03 (atom 378) Step -1, time -0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000001, max 0.000005 (between atoms 775 and 776) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 262 263 30.3 0.1000 0.1000 0.1000 Step 212, Epot=-1.233691e+04, Fnorm=4.926e+01, Fmax=5.858e+02 (atom 378) Step 213, Epot=-1.234682e+04, Fnorm=8.846e+01, Fmax=1.130e+03 (atom 261) Step 214, Epot=-1.235149e+04, Fnorm=8.846e+01, Fmax=1.372e+03 (atom 262) writing lowest energy coordinates. Back Off! I just backed up em_cg_constrain_vacuum.gro to ./#em_cg_constrain_vacuum.gro.1# Polak-Ribiere Conjugate Gradients converged to Fmax < 100 in 275 steps Potential Energy = -1.25808627767813e+04 Maximum force = 9.11707505025239e+01 on atom 757 Norm of force = 1.65933958355887e+01 I constraint h-bond in cg.mdp: title = bovin cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = h-bonds integrator = cg dt = 0.002 ; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes emtol = 100 emstep = 0.001 ; Highest order in the expansion of the constraint coupling matrix lincs_order = 8 ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = no gen-temp = 293 gen-seed = 173529 in order to fix warning, I use distance_restraints as follows: genrestr -f em_xxx.gro -o posre.itp -disre_dist 0.1 -disre_up2 1 acording to the posre.itp, revise xxx.top file, ; Include Position restraint file #ifdef POSRES #include "posre.itp" [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 1 4 1 0 2 0.0 0.19 1.19 1.0 181 182 1 0 2 0.0 0.19 1.19 1.0 262 263 1 0 2 0.0 0.19 1.19 1.0 296 297 1 0 2 0.0 0.19 1.19 1.0 353 354 1 0 2 0.0 0.23 1.23 1.0 512 516 1 1 2 0.0 0.24 1.24 1.0 685 688 1 0 2 0.0 0.19 1.19 1.0 775 776 1 0 2 0.0 0.20 1.20 1.0 994 995 1 2 2 0.0 0.24 1.24 1.0 #endif But things not changed, same warning How should I do to fix it? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists