I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0
I am not sure about rlist. Regards, Tarak On Fri, May 17, 2013 at 1:46 PM, tarak karmakar <tarak20...@gmail.com> wrote: > 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://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> >>>>>> >>>> >>>> -- >>>> ======================================== >>>> >>>> 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 >>>> >>>> ======================================== >>>> -- >>>> 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? 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