I get an error like this= Step 43230, time 86.46 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.033583, max 1.621884 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.0 0.4449 0.2622 0.1000 2031 2030 90.0 0.1949 0.1264 0.1000 Wrote pdb files with previous and current coordinates
Step 43231, time 86.462 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.066301, max 3.173023 (between atoms 2032 and 2030) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2032 2030 90.0 0.2622 0.4173 0.1000 2031 2030 89.9 0.1264 0.1675 0.1000 ------------------------------------------------------- Program mdrun, VERSION 4.5.3 Source code file: constr.c, line: 176 Fatal error: Too many LINCS warnings (1001) 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 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- and my md.mdp file i altered goes like this= ; VARIOUS PREPROCESSING OPTIONS title = Production Simulation cpp = /lib/cpp ; RUN CONTROL PARAMETERS integrator = md tinit = 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 2500000 ; Make it 10 ns ; OUTPUT CONTROL OPTIONS nstxout = 500 ; Writing full precision coordinates every nanosecond nstvout = 500 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 2500 ; Writing to the log file every step nstenergy = 2500 ; Writing out energy information every step nstxtcout = 500 ; Writing coordinates every 5 ps energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r = 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 how should i rectify this. Please help On Sun, Dec 18, 2011 at 8:12 PM, Mark Abraham <[email protected]>wrote: > On 19/12/2011 1:05 AM, aiswarya pawar wrote: > > Hi users, > > I did energy minimization of a protein complex using the following > minimization mdp file. > > > See > http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulationfor > general advice. > > > > ; Lines starting with ';' ARE COMMENTS > ; Everything following ';' is also comment > > title = Energy Minimization ; Title of run > > ; The following line tell the program the standard locations where to > find certain files > cpp = /lib/cpp ; Preprocessor > > > ; Define can be used to control processes > define = -DFLEXIBLE > > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < 1.0 kJ/mol > emstep = 0.01 > nsteps = 5000 ; Maximum number of (minimization) steps to perform > nstenergy = 10 ; Write energies to disk every nstenergy steps > energygrps = Protein ; Which energy group(s) to write to disk > > ; Parameters describing how to find the neighbors of each atom and how > to calculate the interactions > nstlist = 10 ; Frequency to update the neighbor list and long range forces > ns_type = grid ; Method to determine neighbor list (simple, grid) > rlist = 1.0 ; Cut-off for making neighbor list (short range forces) > coulombtype = PME ; Treatment of long range electrostatic interactions > rcoulomb = 1.0 ; long range electrostatic cut-off > rvdw = 1.4 ; long range Van der Waals cut-off > constraints = none ; Bond types to replace by constraints > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > > and the pr.mdp = > > ; VARIOUS PREPROCESSING OPTIONS > title = Position Restrained Molecular Dynamics > define = -DPOSRES > > constraints = all-bonds > integrator = md > dt = 0.001 ; ps ! > nsteps = 25000 ; total 50 ps. > nstcomm = 10 > nstxout = 500 ; collect data every 1 ps > nstxtcout = 500 > nstvout = 0 > nstfout = 0 > nstlist = 10 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.4 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > DispCorr = no > ; Berendsen temperature coupling is on > Tcoupl = v-rescale > tau_t = 0.1 0.1 > tc-grps = protein non-protein > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = parrinello-rahman > Pcoupltype = isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = -1 > > > You are asking for trouble by generating velocities and doing position > restraints with P-R pressure coupling in one step. It might work, but the > workflow in the above link is safer. > > > > and md.mdp file = > > ; VARIOUS PREPROCESSING OPTIONS > title = Position Restrained Molecular Dynamics > > > ; RUN CONTROL PARAMETERS > constraints = all-bonds > integrator = md > dt = 0.002 ; 2fs ! > nsteps = 2500000 ; total 5000 ps. > nstcomm = 10 > nstxout = 500 ; collect data every 1 ps > nstxtcout = 0 > nstvout = 0 > nstfout = 0 > nstlist = 10 > ns_type = grid > rlist = 1.0 > coulombtype = PME > rcoulomb = 1.0 > vdwtype = cut-off > rvdw = 1.4 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > DispCorr = no > ; Berendsen temperature coupling is on > Tcoupl = v-rescale > tau_t = 0.1 0.1 > tc-grps = protein non-protein > ref_t = 300 300 > ; Pressure coupling is on > Pcoupl = parrinello-rahman > Pcoupltype = isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = -1 > > > Why are you re-generating non-equilibrium velocities after equilibrating > them? > > Mark > > > > > The minimization step went well. but while doing the final mdrun am > getting LINCS error. i read through the numerous mailing list on grimaces > but still couldn't understand how would i fix this. am getting this error > for all the 10 protein complex i did minimization for. Please help. > > > Thanks, > Aiswarya > > > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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