Now if I increase the rlist it is showing that With coulombtype = PME, rcoulomb must be equal to rlist If you want optimal energy conservation or exact integration use PME-Switch
I don't know exactly what will be the best set up with charmm force field. Any suggestion please!! Thanks, Tarak On Fri, May 17, 2013 at 1:34 PM, tarak karmakar <tarak20...@gmail.com>wrote: > 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
