What about Dispersion Correction ? But if I use this set of informations ; 7.3.3 Run Control integrator = md ; md integrator tinit = 0 ; [ps] starting time for run dt = 0.001 ; [ps] time step for integration nsteps = 5000000 ; maximum number of steps to integrate, 0.001 * 50,00,000 =5 ns nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = system ; group(s) for center of mass motion removal comm_mode = linear
; 7.3.8 Output Control nstxout = 5000 ; [steps] freq to write coordinates to trajectory nstvout = 5000 ; [steps] freq to write velocities to trajectory nstfout = 5000 ; [steps] freq to write forces to trajectory nstlog = 1000 ; [steps] freq to write energies to log file nstenergy = 1000 ; [steps] freq to write energies to energy file nstxtcout = 1000 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps = System ; group(s) to write to xtc trajectory energygrps = protein ligand ; 7.3.9 Neighbor Searching nstlist = 10 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list rlistlong = 1.4 ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb = 1.2 ; [nm] distance for Coulomb cut-off fourierspacing = 0.16 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.11 VdW vdwtype = switch ; twin-range cut-off with rlist where rvdw >= rlist rvdw = 1.2 ; [nm] distance for LJ cut-off rvdw-switch = 1.0 DispCorr = Ener ; apply long range dispersion corrections for energy ; 7.3.14 Temperature Coupling tcoupl = nose-hoover ; temperature coupling tc_grps = system ; groups to couple seperately to temperature bath tau_t = 1.0 ; [ps] time constant for coupling ref_t = 300 ; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 1.0 ; [ps] time constant for coupling compressibility = 4.5e-5 ; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling gen_vel = yes ; velocity generation gen_temp = 300 gen_seed = 8877691 ; 7.3.18 Bonds constraints = h-bonds ; covalent h-bonds constraints constraint_algorithm = LINCS ; LINear Constraint Solver continuation = yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30 ; [degrees] maximum angle that a bond can rotate before LINCS will complain It is showing the following warning "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw." On Sun, May 12, 2013 at 11:57 PM, tarak karmakar <tarak20...@gmail.com>wrote: > Oh ! > Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp. > Restrains things I didn't follow properly, anyway I'll read about this. > > > On Sun, May 12, 2013 at 11:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/12/13 1:53 PM, tarak karmakar wrote: >> >>> Thanks, >>> >>> I have used CGENFF force field parameters for the ligand generated from >>> PARMCHEM with 0 penalties. For protein I have used CHARMM36 force field. >>> my npt.mdp file is as follows, >>> >>> ; 7.3.3 Run Control >>> integrator = md >>> >> >> Bug 1021 was only relevant with md-vv, so it is not your problem here. >> >> >> tinit = 0 >>> dt = 0.001 >>> nsteps = 5000000 >>> nstcomm = 1 >>> comm_grps = system >>> comm_mode = linear >>> >>> >>> ; 7.3.8 Output Control >>> nstxout = 5000 >>> nstvout = 5000 >>> nstfout = 5000 >>> nstlog = 1000 >>> nstenergy = 1000 >>> nstxtcout = 1000 >>> xtc_precision = 1000 >>> xtc_grps = System >>> energygrps = lIG Protein Water >>> >>> ; 7.3.9 Neighbor Searching >>> nstlist = 10 >>> ns_type = grid >>> pbc = xyz >>> rlist = 1.2 >>> >>> ; 7.3.10 Electrostatics >>> coulombtype = PME >>> rcoulomb = 1.2 >>> >>> ; 7.3.11 VdW >>> vdwtype = cut-off >>> rvdw = 1.2 >>> DispCorr = EnerPres >>> >>> >> Your short-range settings are incorrect for strict use of CHARMM. You >> should set: >> >> vdwtype = switch >> rvdw-switch = 1.0 >> rlistlong = 1.4 >> >> Your other settings for rlist, rcoulomb, and rvdw are fine. >> >> >> ; 7.3.13 Ewald >>> fourierspacing = 0.12 >>> pme_order = 4 >>> ewald_rtol = 1e-5 >>> >>> ; 7.3.14 Temperature Coupling >>> tcoupl = nose-hoover >>> tc_grps = system >>> tau_t = 1.0 >>> ref_t = 300 >>> >>> ; 7.3.15 Pressure Coupling >>> pcoupl = parrinello-rahman >>> pcoupltype = isotropic >>> tau_p = 1.0 >>> compressibility = 4.5e-5 >>> ref_p = 1.0 >>> >>> gen_vel = yes >>> >> >> In the absence of any restraints, initial velocity generation can produce >> incorrect dynamics. This is why we use restraints. Thus far, your >> observations simply seem consistent with random effects of improper >> nonbonded parameters and/or equilibration. >> >> -Justin >> >> gen_temp = 300 >>> gen_seed = 8877691 >>> >>> ; 7.3.18 Bonds >>> constraints = h-bonds >>> constraint_algorithm = LINCS >>> continuation = yes >>> lincs_order = 4 >>> lincs_warnangle = 30 >>> >>> >>> On Sun, May 12, 2013 at 11:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 5/12/13 1:34 PM, tarak karmakar wrote: >>>> >>>> Thanks Justin for the Quick and Helpful reply. >>>>> >>>>> Yes. If I am right, the chaotic behavior of the simulations is >>>>> inherent >>>>> and can be assessed statistically by generating several independent >>>>> trajectories and analyzing their similar outcomes. But with the same >>>>> '.mdp' >>>>> file I am getting TOO much different results, and that's where I worry. >>>>> I'll surely try with the recent version of gromacs. But, for now, can >>>>> you >>>>> give me a little more informations about problems (bugs) with the 4.5.5 >>>>> version, related to my context? >>>>> >>>>> >>>>> The proposed relationship to bug 1012 is unclear to me. The issue >>>> there >>>> was an incompatibility between an integrator and thermostat, with >>>> obvious >>>> differences in thermodynamic output. Assessing your system in this >>>> context >>>> is not helpful. If you want to assess whether different core counts or >>>> hardware produce problems, then you need a very simple test case (like a >>>> box of water) that shows significant differences in averaged >>>> observables. >>>> As I said before, maybe your ligand parameters are insufficiently >>>> accurate >>>> (how did you generate them?) or .mdp settings are incorrect. Without >>>> such >>>> information, there is little point in trying to debug anything. >>>> >>>> >>>> -Justin >>>> >>>> -- >>>> ==============================****========== >>>> >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Research Scientist >>>> Department of Biochemistry >>>> Virginia Tech >>>> Blacksburg, VA >>>> jalemkul[at]vt.edu | (540) 231-9080 >>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<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<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> > >>>> * Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<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<http://www.gromacs.org/**Support/Mailing_Lists> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >> -- >> ==============================**========== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > > > > -- 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
