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
