I am using the opls parameters from Lope's paper. In vaccum energy minimzatin is working well. MD is not at all working.
My other systems are running well. In the present system I changed the anion, cation parameters are fine. Is the problem with anion parameters? Nilesh On Fri, June 4, 2010 10:20 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I am trying to equilibrate my system, ionic liquids. My simulations >> gets stop immediately. I reduced the step size. I modified initial >> structure. I changed the box size. I checked force field parameters. I >> am using opls foce field. I repeated my energy minimization 2-3 times. I >> could not solve the problem. Every time i am geting following error >> message. >> >> step 0Warning: 1-4 interaction between 20 and 27 at distance 3.803 >> which is larger than the 1-4 table size 2.400 nm These are ignored for >> the rest of the simulation This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file or with user >> tables increase the table size Segmentation fault >> >> >> >> >> Can you tell me how to solve this problem. >> > > Please consult the following: > > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an > _Unstable_System > > > The prime suspect in my mind is your topology. How have you validated > the parameters for your ionic liquids? Does in vacuo minimization and > short MD of each component separately run stably? While OPLS is quite > versatile, parameterizing ionic liquids properly is not a trivial task, > and is probably not very straightforward. > > -Justin > > >> Here I have pasted the eqilibration file. >> Nilesh >> >> >> title = cpeptid position restraining cpp >> = /usr/bin/cpp >> constraints = none integrator = md dt >> = 0.001 ; ps ! >> nsteps = 100000 ; total 1.0 ps. nstcomm = >> 1 >> nstxout = 10000 nstvout = 10000 nstfout >> = 0 >> nstlog = 10 nstenergy = 10 nstlist = >> 10 >> ns_type = grid rlist = 1.0 coulombtype >> = PME >> vdwtype = cut-off rcoulomb = 1.0 rvdw >> = 1.4 >> fourierspacing = 0.12 fourier_nx = 0 fourier_ny >> = 0 >> fourier_nz = 0 pme_order = 4 ewald_rtol = >> 1e-5 >> optimize_fft = yes ; Berendsen temperature coupling is on >> Tcoupl = v-rescale >> tau_t = 0.1 tc-grps =system ref_t = 300 ; Pressure coupling is on >> Pcoupl = parrinello-rahman >> pcoupltype = isotropic tau_p = 0.5 compressibility >> = 4.5e-5 >> ref_p = 1.0 ; Generate velocites is on at 300 K. >> gen_vel = yes gen_temp = 300.0 gen_seed >> = 173529 >> >> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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/mailing_lists/users.php > > > -- 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/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/mailing_lists/users.php
