Thank you Justin for your answer. I'm trying to add the position restraints to my protein, but I have a problem. My topology is made of a chain repeated twice and if I want to build the position restraints through genrestr from a gro file, the numeration of the atoms would put the 2 chains sequentially one after the other, but then the index would be out of bounds; if I try to generate the topology from x2top it has been taking more than 6 hours and hasn't finish yet. If instead I try to use the posre.itp built from pdb2gmx I still have the LINCS warnings, even after changing rlist, rcoulomb and rvdw to 1. Any ideas on a faster way to add my position restraints or how to solve the LINCS error? Thank you very much. Francesca
2012/3/29 Justin A. Lemkul <jalem...@vt.edu>: > > > francesca vitalini wrote: >> >> My minimization was done without any constraints. I'm starting using >> constraints only in the nvt equilibration as I'm trying to equilibrate >> my solvent, so, maybe here I'm being extremely naďve, but, shouldn't I >> >> avoid fixing the water in the nvt, as equilibrating it is exactly the >> reason I'm running the nvt equilibration? Or am I misunderstanding >> something? > > > You should likely be restraining your protein, not the water. Bad initial > geometry (sometimes stuff survives EM) can give your structure a nasty kick > that causes things to spin out of control. Restraints on the protein > mitigate these effects while the water relaxes. > > -Justin > > >> Thanks >> Francesca >> >> >> >> 2012/3/29 <chris.ne...@utoronto.ca>: >>> >>> I didn't follow this whole thread, but I sometimes need to turn off all >>> constraints when doing minimization. In fact, for that reason I entirely >>> stopped ever using restraints during energy minimization. In extreem >>> cases, >>> I have had success also by forcing the water to be flexible with a >>> -DFLEXIBLE (or whatever is appropriate for your water model; check the >>> .itp) >>> statement in the .mdp file. >>> >>> Once EM is done, use rigid water and restraints and everything works out >>> ok. >>> >>> Chris. >>> >>> -- original message -- >>> >>> Hallo Felix, >>> thank you for your answer. I tried the constraints = h-bonds but no >>> change in the output. If I look at the step.pdb file that is produced >>> after the running I have some strange outcome. For example some of my >>> atoms are not recognized as part of my protein any more and my >>> structure is destroied. Am I using some strange parameters for nvt >>> without realizing it? I've started from the mdp file provided by the >>> lysozyme tutorial non the Gromacs webpage. >>> if anyone has any ideas it is more than welcome. >>> Francesca >>> >>> integrator = md ; leap-frog integrator >>> nsteps = 10000 ; 2 * 10000 = 20 ps >>> dt = 0.002 ; 2 fs >>> ; Output control >>> nstxout = 1 ; save coordinates every 0.2 ps >>> nstvout = 1 ; save velocities every 0.2 ps >>> nstenergy = 50 ; save energies every 0.2 ps >>> nstlog = 50 ; update log file every 0.2 ps >>> ; Bond parameters >>> unconstrained_start = no >>> ;continuation = no ; first dynamics run >>> constraint_algorithm = lincs ; holonomic constraints >>> constraints = h-bonds ; all bonds (even heavy atom-H bonds) >>> constrained >>> lincs_iter = 1 ; accuracy of LINCS >>> lincs_order = 4 ; also related to accuracy >>> ; Neighborsearching >>> ns_type = grid ; search neighboring grid cells >>> nstlist = 5 ; 10 fs >>> rlist = 3.0 ; short-range neighborlist cutoff (in nm) >>> rcoulomb = 3.0 ; short-range electrostatic cutoff (in >>> nm) >>> rvdw = 3.0 ; short-range van der Waals cutoff (in >>> nm) >>> ; Electrostatics >>> coulombtype = PME ; Particle Mesh Ewald for long-range >>> electrostatics >>> pme_order = 4 ; cubic interpolation >>> fourierspacing = 0.16 ; grid spacing for FFT >>> ; Temperature coupling is on >>> tcoupl = berendsen ; modified Berendsen thermostat >>> tc-grps = Protein Non-Protein ; two coupling groups - more >>> accurate >>> tau_t = 0.1 0.1 ; time constant, in ps >>> ref_t = 300 300 ; reference temperature, one >>> for each group, in K >>> ; Pressure coupling is off >>> pcoupl = no ; no pressure coupling in NVT >>> ; Periodic boundary conditions >>> pbc = xyz ; 3-D PBC >>> ; Dispersion correction >>> DispCorr = EnerPres ; account for cut-off vdW scheme >>> ; Velocity generation >>> gen_vel = yes ; assign velocities from Maxwell >>> distribution >>> gen_temp = 300 ; temperature for Maxwell distribution >>> gen_seed = -1 ; generate a random seed >>> >>> >>> >>> 2012/3/29 Rausch, Felix <frau...@ipb-halle.de>: >>> >>> [Hide Quoted Text] >>> Hello again, >>> >>> Well, I once had problems with simulations crashing randomly during >>> production runs (sometimes after tens of nanoseconds) with the LINCS >>> warnings you described. Switching LINCS from "all-bonds" to only >>> "h-bonds" >>> did the trick for me, although I never exactly figured out why. >>> Maybe it's worth a try for you, too? >>> Cheers, >>> Felix >>> >>> -----Ursprüngliche Nachricht----- >>> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >>> Im >>> Auftrag von francesca vitalini >>> Gesendet: Donnerstag, 29. März 2012 15:15 >>> An: Discussion list for GROMACS users >>> Betreff: Re: [gmx-users] Not able to continue with Equilibration >>> >>> Hi! >>> I'm having a similar problem. I have a dimer solvated in a big box of >>> water >>> plus ions that I have managed to minimize correctly (see output of >>> minimization at the end) but when I try to run NVT equilibration (see >>> later) >>> I get LINCS warnings(see below) refearred to atoms which are not in a >>> cluster or in a strange position. I have added dihedral restraints on >>> them >>> but still the same type of error. I'm using GROMACS 3.3.1. I have tried >>> to >>> switch to a newer version of GROMACS but still the same error. >>> Does anyone have any suggestions? >>> Thanks >>> Francesca >>> >>> >>> MINIMIZATION OUTPUT >>> >>> Steepest Descents converged to Fmax < 1000 in 681 steps Potential Energy >>> = >>> -1.9597512e+07 >>> Maximum force = 2.4159846e+02 on atom 13087 >>> Norm of force = 2.1520395e+04 >>> >>> >>> MINIMIZATION.MDP >>> >>> define = -DEFLEXIBLE ; flexible water >>> integrator = steep ; Algorithm (steep = steepest descent >>> minimization) >>> emtol = 1000.0 ; Stop minimization when the maximum >>> force < 1000.0 kJ/mol/nm >>> emstep = 0.001 ; Energy step size >>> nsteps = 50000 ; Maximum number of (minimization) >>> steps to perform >>> >>> ; Parameters describing how to find the neighbors of each atom and how to >>> calculate the interactions >>> nstlist = 1 ; 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 ; Short-range electrostatic cut-off >>> rvdw = 1.0 ; Short-range Van der Waals cut-off >>> pbc = xyz ; Periodic Boundary Conditions (yes/no) >>> >>> >>> NVT.MDP >>> >>> define = -DPOSRES ; position restrain the protein >>> ; Run parameters >>> integrator = md ; leap-frog integrator >>> nsteps = 10000 ; 2 * 10000 = 20 ps >>> dt = 0.002 ; 2 fs >>> ; Output control >>> nstxout = 50 ; save coordinates every 0.2 ps >>> nstvout = 50 ; save velocities every 0.2 ps >>> nstenergy = 50 ; save energies every 0.2 ps >>> nstlog = 50 ; update log file every 0.2 ps >>> ; Bond parameters >>> unconstrained_start = no >>> ;continuation = no ; first dynamics run >>> constraint_algorithm = lincs ; holonomic constraints >>> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >>> constrained >>> lincs_iter = 1 ; accuracy of LINCS >>> lincs_order = 4 ; also related to accuracy >>> ; Neighborsearching >>> ns_type = grid ; search neighboring grid cells >>> nstlist = 5 ; 10 fs >>> rlist = 3.0 ; short-range neighborlist cutoff (in nm) >>> rcoulomb = 3.0 ; short-range electrostatic cutoff (in >>> nm) >>> rvdw = 3.0 ; short-range van der Waals cutoff (in >>> nm) >>> ; Electrostatics >>> coulombtype = PME ; Particle Mesh Ewald for long-range >>> electrostatics >>> pme_order = 4 ; cubic interpolation >>> fourierspacing = 0.16 ; grid spacing for FFT >>> ; Temperature coupling is on >>> tcoupl = berendsen ; modified Berendsen thermostat >>> tc-grps = Protein Non-Protein ; two coupling groups - more >>> accurate >>> tau_t = 0.1 0.1 ; time constant, in ps >>> ref_t = 300 300 ; reference temperature, one >>> for each group, in K >>> ; Pressure coupling is off >>> pcoupl = no ; no pressure coupling in NVT >>> ; Periodic boundary conditions >>> pbc = xyz ; 3-D PBC >>> ; Dispersion correction >>> DispCorr = EnerPres ; account for cut-off vdW scheme >>> ; Velocity generation >>> gen_vel = yes ; assign velocities from Maxwell >>> distribution >>> gen_temp = 300 ; temperature for Maxwell distribution >>> gen_seed = -1 ; generate a random seed >>> >>> ; Dihedral restraints >>> >>> dihre = simple ; Some dihedrals are restrained for >>> instance peptide bonds are set to trans conformation. >>> dihre_fc = 500 >>> dihre_tau = 0.0 >>> nstdihreout = 50 >>> >>> NVT LINCS ERROR >>> >>> Step 0, time 0 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 0.002851 (between atoms 10721 and 10723) rms 0.000161 bonds that >>> rotated >>> more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 672 673 33.7 0.1000 0.1000 0.1000 >>> 1081 1082 33.8 0.1000 0.1000 0.1000 >>> 1647 1648 34.4 0.1000 0.1000 0.1000 >>> 2819 2820 37.1 0.1000 0.1000 0.1000 >>> 2920 2921 39.6 0.1000 0.1000 0.1000 >>> 4090 4091 35.2 0.1000 0.1000 0.1000 >>> 4727 4728 37.2 0.1000 0.1000 0.1000 >>> 5160 5161 31.7 0.1000 0.1000 0.1000 >>> 6824 6825 33.3 0.1000 0.1000 0.1000 >>> ... >>> step 0 >>> Step 1, time 0.002 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 0.017976 (between atoms 14692 and 14693) rms 0.000520 bonds that >>> rotated >>> more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 672 673 67.8 0.1000 0.0999 0.1000 >>> .... >>> >>> Step 2, time 0.004 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 0.060681 (between atoms 6906 and 6907) rms 0.001874 bonds that >>> rotated >>> more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 672 673 80.8 0.0999 0.0999 0.1000 >>> 1081 1082 90.0 0.1000 0.1008 0.1000 >>> ... >>> >>> Step 3, time 0.006 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 0.104238 (between atoms 10603 and 10604) rms 0.003281 bonds that >>> rotated >>> more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 672 673 67.1 0.0999 0.1000 0.1000 >>> 1081 1082 69.6 0.1008 0.1000 0.1000 >>> ... >>> >>> Step 4, time 0.008 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 0.569872 (between atoms 8709 and 8710) rms 0.013041 bonds that >>> rotated >>> more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 672 673 40.3 0.1000 0.1000 0.1000 >>> 1081 1082 39.6 0.1000 0.1000 0.1000 >>> 1249 1250 37.6 0.1000 0.1000 0.1000 >>> ... >>> >>> Step 5, time 0.01 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 2.761976 (between atoms 8202 and 8204) rms 0.056483 bonds that >>> rotated >>> more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 3320 3321 43.0 0.1090 0.1090 0.1090 >>> 3875 3876 32.0 0.1090 0.1090 0.1090 >>> 4013 4014 34.3 0.1090 0.1082 0.1090 >>> 4070 4071 42.1 0.1092 0.1092 0.1090 >>> 4072 4073 45.2 0.1090 0.1086 0.1090 >>> 4727 4729 34.2 0.1007 0.1002 0.1000 >>> 4961 4962 31.4 0.1091 0.1089 0.1090 >>> 4992 4993 46.0 0.1091 0.1089 0.1090 >>> 8159 8160 30.9 0.1251 0.1465 0.1230 >>> ... >>> >>> Step 6, time 0.012 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 22.009092 (between atoms 8202 and 8204) rms 0.488487 bonds that >>> rotated >>> more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 2920 2921 44.7 0.1000 0.1001 0.1000 >>> 3320 3321 36.6 0.1090 0.1087 0.1090 >>> 3592 3593 32.1 0.1090 0.1089 0.1090 >>> .... >>> Warning: 1-4 interaction between 8159 and 8168 at distance 1.580 which is >>> larger than the 1-4 table size 1.000 nm These are ignored for the rest of >>> the simulation This usually means your system is exploding, if not, you >>> should increase table-extension in your mdp file >>> >>> Step 7, time 0.014 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 403.393890 (between atoms 8202 and 8204) rms 8.430617 bonds that >>> rotated >>> more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 302 303 31.7 0.1003 0.1001 0.1000 >>> 672 673 66.4 0.1001 0.1001 0.1000 >>> 1050 1051 33.1 0.1003 0.1003 0.1000 >>> 1081 1082 46.7 0.1000 0.1000 0.1000 >>> 1225 1226 35.0 0.1003 0.1003 0.1000 >>> .... >>> >>> Wrote pdb files with previous and current coordinates >>> >>> Step 8, time 0.016 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 7568.298828 (between atoms 8202 and 8204) rms 155.435715 bonds that >>> rotated more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length >>> 205 206 31.6 0.1003 0.1002 0.1000 >>> 302 303 36.9 0.1001 0.1002 0.1000 >>> 672 673 76.0 0.1001 0.0997 0.1000 >>> 1050 1051 34.3 0.1003 0.1003 0.1000 >>> 1081 1082 63.0 0.1000 0.0999 0.1000 >>> 1225 1226 36.6 0.1003 0.1003 0.1000 >>> 1249 1250 38.7 0.1001 0.1001 0.1000 >>> 1647 1648 62.8 0.1000 0.0996 0.1000 >>> 1679 1680 42.5 0.1000 0.1000 0.1000 >>> 2214 2215 31.6 0.1002 0.1001 0.1000 >>> 2577 2578 31.1 0.1003 0.1002 0.1000 >>> 2819 2820 68.0 0.1000 0.0997 0.1000 >>> 2920 2921 71.5 0.1023 0.1000 0.1000 >>> 3468 3469 34.7 0.1092 0.1090 0.1090 >>> 3676 3677 34.7 0.1090 0.1090 0.1090 >>> 3714 3717 34.7 0.0998 0.0999 0.1000 >>> 3746 3747 70.8 0.1086 0.1069 0.1090 >>> .... >>> >>> Back Off! I just backed up step7.pdb to ./#step7.pdb.1# Wrote pdb files >>> with >>> previous and current coordinates >>> >>> Step 9, time 0.018 (ps) LINCS WARNING >>> relative constraint deviation after LINCS: >>> max 148599.687500 (between atoms 8202 and 8204) rms 3002.328125 bonds >>> that >>> rotated more than 30 degrees: >>> atom 1 atom 2 angle previous, current, constraint length .... >>> >>> Back Off! I just backed up step8.pdb to ./#step8.pdb.1# Wrote pdb files >>> with >>> previous and current coordinates Segmentation fault >>> >>> >>> 2012/3/29 Mark Abraham <mark.abra...@anu.edu.au>: >>> On 29/03/2012 8:22 PM, Hendry wrote: >>> >>> Hi, >>> >>> >>> >>> I am using Gromacs 4.5.4. After successful minimization by SD, I >>> continued with equilibration step but I got the below errors. I tried >>> many times with different parameters but the problem still persists. I >>> have given errors and md parameters of equilibration step below. I >>> have also provided my minimization output at the end. Could you >>> provide some suggestions what went wrong?. >>> >>> >>> You are using PR-pressure coupling for equilibration, which is an >>> unstable combination. You are coupling ions to their own thermostat, >>> which is unstable. Do check out the GROMACS manual for discussion of >>> how these algorithms work, and also the website for some practical >>> observations. >>> >>> Mark >>> >>> - >>> >>> >>> -- >>> 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 thewww >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > 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 -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412 -- 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
