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 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 ; 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 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> > -- 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
