Dear Justin, Thanks.
I tried to equilibrate the system in NVT ensemble without constraints, the equilibration completed, but the lipid layers moved apart, so i tried to do simulated annealing procedure mentioned in the trouble shooting section of the tutorial and here also i was able to equilibrate only with the constraints = none option in anneal_npt.mdp file (below). title = Simulated Annealing define = -DPOSRES -DPOSRES_LIPID integrator = md dt = 0.001 nsteps = 500000 continuation = no constraints = none constraint-algorithm = lincs lincs-iter = 1 lincs-order = 4 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstenergy = 1000 nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 coulombtype = PME pme_order = 4 fourierspacing = 0.16 Tcoupl = Berendsen tc_grps = Protein DPPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 323 323 323 Pcoupl = Berendsen Pcoupltype = semiisotropic ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = no pbc = xyz DispCorr = EnerPres nstcomm = 1 comm-mode = Linear comm-grps = Protein_DPPC SOL_CL- annealing = single single single annealing_npoints = 2 2 2 annealing_time = 0 500 0 500 0 500 annealing_temp = 0 323 0 323 0 323 Now as i would like to proceed further, please suggest me how to confirm that the simulated annealing was proper and also please let me know can i now go to npt equillibration using the output of simulated annealing as input to npt equilibration. Like I am going to use the following command to run the npt equillibration: grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n index.ndx -o npt.tpr Thanks, Ram On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks and I tried your suggestion, that is minimizing the system >> without restraints and increasing the Fmax to 1000, the mdp file used >> is as follows: >> > > Note that I only suggested EM, not necessarily Fmax < 1000. You original > post contained an even lower Fmax, suggesting that you can do better than > 1000. The parameters in my tutorial are somewhat generic; you should alter > them to suit your needs. > > <snip> > > Please note that the headers of log files are typically unnecessary when > posting the .mdp file. > >> please suggest me is it ok to remove the constraints and run the NVT >> equillibration. >> > > You can try it, but I doubt it will make a difference. Your simulation is > crashing before it is even starting, making it very difficult to diagnose. > You probably need to re-build the system, using as rigorous criteria as > possible during the InflateGRO steps to ensure that you don't have any > improper atomic overlap. In my experience, if the simulation is failing at > step 0, there is no hope for coaxing the system into working. The > configuration simply isn't reasonable. > > -Justin > >> Thanks >> >> Ram >> >> >> >> >> >> >> >> On Fri, Oct 16, 2009 at 9:27 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> ram bio wrote: >>>> >>>> Dear Gromacs users, >>>> >>>> I am doing protein in lipid-bilayer simulation and i am following the >>>> procedure as per justin tutorial. I am able to insert the protein in >>>> lipid bilayer and minimize the system as per Inflategro >>>> procedure,during the total procedure the system was minimized in every >>>> step.Then, I solvated and ionized sytem and minimized using the >>>> following mdp file: >>>> >>>> ; minim.mdp - used as input into grompp to generate em.tpr >>>> ; Parameters describing what to do, when to stop and what to save >>>> define = -DSTRONG_POSRES >>>> integrator = steep ; Algorithm (steep = steepest descent >>>> minimization) >>>> emtol = 500.0 ; Stop minimization when the maximum >>>> force < 1000.0 kJ/mol/nm >>>> emstep = 0.01 ; 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 = 1.2 ; Cut-off for making neighbor list >>>> (short range forces) >>>> coulombtype = PME ; Treatment of long range >>>> electrostatic interactions >>>> rcoulomb = 1.2 ; Short-range electrostatic cut-off >>>> rvdw = 1.2 ; Short-range Van der Waals cut-off >>>> pbc = xyz ; Periodic Boundary Conditions (yes/no) >>>> >>>> the output was as follows: >>>> >>>> Steepest Descents converged to Fmax < 500 in 4770 steps >>>> Potential Energy = -3.8820288e+05 >>>> Maximum force = 4.4803549e+02 on atom 3573 >>>> Norm of force = 1.7854408e+01 >>>> >>>> As the potential energy and Fmax values were agreeable , I proceeded >>>> to equillibrate the system using NVT. >>>> >>> Did you minimize the structure without restraints, prior to NVT? >>> >>> <snip> >>> >>>> Angle G96Angle Proper Dih. Ryckaert-Bell. Improper >>>> Dih. >>>> 2.20077e+04 8.54042e+03 6.78950e+03 4.34650e+03 >>>> 3.03266e+03 >>>> LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb >>>> (SR) >>>> 4.76527e+03 5.50236e+04 8.36617e+06 -2.20019e+03 >>>> -4.46844e+05 >>>> Coul. recip. Position Rest. Potential Kinetic En. Total >>>> Energy >>>> -1.65524e+05 1.07769e+01 7.85612e+06 5.88813e+10 >>>> 5.88892e+10 >>>> Conserved En. Temperature Pressure (bar) Cons. rmsd () >>>> 5.88892e+10 2.23805e+08 1.21713e+09 3.10245e+01 >>>> >>> In my experience, the combination of an astronomically high temperature >>> and >>> a repulsive temperature is indicative of restraining an unrestrainable >>> starting structure. Try the EM I suggested above. Other than that, as >>> I've >>> suggested before, see the Advanced Troubleshooting page I created in the >>> tutorial. >>> >>> -Justin >>> >>>> Please help me to proceed further and let me know where are the >>>> mistakes lying and how to overcome them. >>>> >>>> Thanks in advance, >>>> >>>> Ram >>>> _______________________________________________ >>>> 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/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/mailing_lists/users.php >>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> 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/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/mailing_lists/users.php >>> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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/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/mailing_lists/users.php > _______________________________________________ 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/search before posting! Please don't post (un)subscribe requests to the list. 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