Robin, Easiest way to get it running, with the flexible bond between O and H in methane would be to decrease the time step. I would start with half a femto second time step and see what happens.
All the best Rajesh On Thu, Dec 2, 2010 at 10:11 AM, Robin C. Underwood <[email protected]>wrote: > GMX Users: > > When I run grompp on methanol in water in v. 4.5.3 I get the following > Note: > > NOTE 1 [file methanol.top, line 73]: > The bond in molecule-type MET between atoms 5 OA and 6 HO has an > estimated oscillational period of 9.0e-03 ps, which is less than 10 times > the time step of 1.0e-03 ps. > Maybe you forgot to change the constraints mdp option. > > Here is my mdp file: > > ; User Robin > ; Wed Dec.1 2010 > ; Input file > ; > title = Yo > cpp = /lib/cpp > integrator = md > dt = 0.001 ; ps ! > nsteps = 1100000 ; total 1000 ps=1 ns > nstcomm = 10 > ; (x) coordinates, (v) is velocities, (f) is forces > ; This affects "traj.trr" > ; these numbers shouldn't be too small (100,000), takes up disk space > nstxout = 1000 > nstvout = 1000 > nstfout = 1000 > ; Output frequency for energies > nstlog = 100 > nstenergy = 100 > ; This affects ".xtc" file for movies this should be a fairly small number > nstxtcout = 100 > xtc-precision = 1000 > ; parameters for neighbors > nstlist = 10 > ns_type = grid > rlist = 0.9 > ; electrostatics > coulombtype = pme > pme_order = 4 > ewald_rtol = 1e-5 > ewald_geometry = 3d > epsilon_surface = 0 > fourierspacing = 0.1 > fourier_nx = 0.0 > fourier_ny = 0.0 > fourier_nz = 0.0 > rcoulomb = 0.9 > optimize_fft = yes > Dispcorr = EnerPres > vdwtype = cutoff > rvdw_switch = 0.85 > rvdw = 0.9 > ; Berendsen temperature coupling is on in two groups > Tcoupl = v_rescale > tc-grps = system > tau_t = 0.1 > ref_t = 300 > ; Energy monitoring > energygrps = MET SOL > ; Isotropic pressure coupling is now on > Pcoupl = berendsen > Pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is off at 300 K. > gen_vel = no > gen_temp = 300.0 > gen_seed = 173529 > > > Here is my top file: > > ; > ; > ; Include forcefield parameters > #include "ffoplsaa.itp" > > ; > ; Methanol, Jorgensen et al. JACS 118 pp. 11225 (1996) > ; > [ moleculetype ] > ; name nrexcl > MET 3 > > [ atoms ] > ; nr type resnr residu atom cgnr charge mass > 1 opls_157 1 MET C 1 0.145 > 2 opls_156 1 MET H 1 0.04 > 3 opls_156 1 MET H 1 0.04 > 4 opls_156 1 MET H 1 0.04 > 5 opls_154 1 MET OA 1 -0.683 > 6 opls_155 1 MET HO 1 0.418 > > [ bonds ] > ; ai aj funct c0 c1 > 1 2 1 > 1 3 1 > 1 4 1 > 1 5 1 > 5 6 1 > > [ pairs ] > ; i j funct > 2 6 > 3 6 > 4 6 > > [ angles ] > ; ai aj ak funct c0 c1 > ; H3 > 2 1 5 1 > 3 1 5 1 > 4 1 5 1 > 4 1 3 1 > 4 1 2 1 > > > [ system ] > ; Name > MET in water > > [ molecules ] > ; Compound #mols > MET 1 > SOL 503 > > > Do I need to add some sort of constraint on my methanol molecule? > > Thanks, > Robin > > > -- > Robin C. Underwood > Chemistry Department > 560 Oval Drive > West Lafayette, IN 47907 > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Naga Rajesh Tummala, PhD School of Chemical, Biological, and Materials Engineering University of Oklahoma
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