Dear Justin, Thanks, will be back after some trials.
Ram On Tue, Oct 20, 2009 at 8:16 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: >> >> Dear Justin, >> >> Thanks for the advice and suggestions, will look into the plots and >> try to run a further NPT equillibration, (here you mean equilibration >> phase 2 ? without annealing, as in the tutorial).. >> > > Yes, normal NPT. > > -Justin > >> Please let me know. >> >> Ram >> >> On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> ram bio wrote: >>>> >>>> Dear Justion, >>>> >>>> When I executed the command g_energy -f anneal_npt1.edr, the output >>>> for temperature and pressure were as under: >>>> >>>> Statistics over 500001 steps [ 0.0000 thru 500.0000 ps ], 1 data sets >>>> All averages are exact over 500001 steps >>>> >>>> Energy Average RMSD Fluct. Drift >>>> Tot-Drift >>>> >>>> >>>> ------------------------------------------------------------------------------- >>>> Temperature 161.41 93.1199 0 0.645591 >>>> 322.796 >>>> Heat Capacity Cv: 24.906 J/mol K (factor = 0.332832) >>>> >>>> Statistics over 500001 steps [ 0.0000 thru 500.0000 ps ], 1 data sets >>>> All averages are exact over 500001 steps >>>> >>>> Energy Average RMSD Fluct. Drift >>>> Tot-Drift >>>> >>>> >>>> ------------------------------------------------------------------------------- >>>> Pressure (bar) -7.96937 115.169 114.406 0.0916656 >>>> 45.8329 >>>> >>>> i am unable to understand from these parameters, whether the system is >>>> ok for future steps. >>> >>> Because simply looking at averages is less useful than looking at the >>> plots. >>> I asked whether the temperature had stabilized, not what it's average >>> value >>> was. Consider this - you're constantly increasing the temperature, so an >>> average is useless. Look at the plot that g_energy gives you and make >>> sure >>> the increase is as you would expect. Probably a further NPT >>> equilibration >>> is needed to make sure that the temperature will remain stable without >>> the >>> influence of annealing. >>> >>> Same thing for pressure - look at the plot. Wide fluctuations will >>> occur, >>> so that's not a problem. The trend is what is important (i.e., running >>> average in xmgrace). Is the pressure leveling off? The average is more >>> meaningful here, and it looks a bit low, but as I advise in my tutorial, >>> equilibrating membrane systems takes a *long* time, anyway. >>> >>> -Justin >>> >>>> Regarding the gaps in the lipid bilayers,now when i visualized the >>>> .trr file in the VMD there were no gaps in the lipid bilayer, that is >>>> they did not move apart. >>>> >>>> Please help. >>>> >>>> Thanks >>>> >>>> Ram >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Tue, Oct 20, 2009 at 7:40 PM, Justin A. Lemkul <jalem...@vt.edu> >>>> wrote: >>>>> >>>>> ram bio wrote: >>>>> >>>>> <snip> >>>>> >>>>>> 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 you would anything else. Have the temperature and pressure >>>>> stabilized? >>>>> Is your structure reasonable (no gaps, etc)? >>>>> >>>>> -Justin >>>>> >>>>>> 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 >>>>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> 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 >>> >> > > -- > ======================================== > > 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. 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