atomtypes.atp FE 55.84700 ; heme iron 56
ffnonbonded FE 9 18.998 0.000 A 0.115816833358244 -0 aminoacids.rtp [ FE ] [ atoms ] FE FE 2.00 0 Hmmmm, confusing... On Thu, Nov 15, 2012 at 3:29 PM, Steven Neumann <s.neuman...@gmail.com> wrote: > Please, see final coordinates. > > 94LIG O1 787 0.482 5.056 3.507 > 94LIG FE 805 0.432 5.011 3.039 > > How is that possible? > > On Thu, Nov 15, 2012 at 3:26 PM, Steven Neumann <s.neuman...@gmail.com> wrote: >> I tried both options and now different atom is responsible of this >> (Oxygen from small molecule next to Fe). With nstxout = 1 I observed >> the trajectory -> My Fe(2+) is coming very close to the Oxygen atom >> and it looks that their coordinate became equal: in VMD Oxygen absorbs >> Fe(2+) and the atom disappears :) Any suggestions? >> >> Steven >> >> On Thu, Nov 15, 2012 at 3:03 PM, Steven Neumann <s.neuman...@gmail.com> >> wrote: >>> :)))))))))))) >>> >>> On Thu, Nov 15, 2012 at 2:58 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> On 11/15/12 9:57 AM, Steven Neumann wrote: >>>>> >>>>> On Thu, Nov 15, 2012 at 2:35 PM, Steven Neumann <s.neuman...@gmail.com> >>>>> wrote: >>>>>> >>>>>> I will. Thank you. >>>>>> >>>>>> Steven >>>>>> >>>>>> On Thu, Nov 15, 2012 at 2:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 11/15/12 9:03 AM, Steven Neumann wrote: >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 11/15/12 8:41 AM, Steven Neumann wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Dear Gmx Users, >>>>>>>>>> >>>>>>>>>> I am trying to run simulations of protein and FE(2+) atoms. I placed >>>>>>>>>> them randomly around the protein, solvated the system and tried to >>>>>>>>>> minimize. After grompp, I tried mdrun: >>>>>>>>>> >>>>>>>>>> Stepsize too small, or no change in energy. >>>>>>>>>> Converged to machine precision, >>>>>>>>>> but not to the requested precision Fmax < 1000 >>>>>>>>>> >>>>>>>>>> Double precision normally gives you higher accuracy. >>>>>>>>>> You might need to increase your constraint accuracy, or turn >>>>>>>>>> off constraints alltogether (set constraints = none in mdp file) >>>>>>>>>> >>>>>>>>>> Steepest Descents converged to machine precision in 62 steps, >>>>>>>>>> but did not reach the requested Fmax < 1000. >>>>>>>>>> Potential Energy = -7.2573600e+05 >>>>>>>>>> Maximum force = 5.7863950e+05 on atom 756 >>>>>>>>>> Norm of force = 3.5862925e+03 >>>>>>>>>> >>>>>>>>>> I tried different stepsizes, constarint = none etc but never >>>>>>>>>> converged >>>>>>>>>> to requested Fmax < 1000 >>>>>>>>>> >>>>>>>>>> When I try NVT: >>>>>>>>>> >>>>>>>>>> Fatal error: >>>>>>>>>> 2 particles communicated to PME node 0 are more than 2/3 times the >>>>>>>>>> cut-off out of the domain decomposition cell of their charge group in >>>>>>>>>> dimension x. >>>>>>>>>> This usually means that your system is not well equilibrated. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> So the problem is with minimization. >>>>>>>>>> >>>>>>>>>> My question: Can it be the problem of not specified vdwradius of my >>>>>>>>>> FE(2+) in vdwradii.dat ? I mean, can ater molecules overlap with >>>>>>>>>> Ferrous and thus minimization does not converge? >>>>>>>>>> >>>>>>>>> >>>>>>>>> The problem is unrelated to vdwradii.dat, which is only used for >>>>>>>>> neighbor >>>>>>>>> searching with genbox. mdrun tells you there is a problem with atom >>>>>>>>> 756. >>>>>>>>> What is it? What is it interacting with? That's how you trace the >>>>>>>>> problem. >>>>>>>>> >>>>>>>>> -Justin >>>>>>>>> >>>>>>>> >>>>>>>> This is Fe(2+) - from trjactory it can be observed that it collides >>>>>>>> with negatively charged oxygen from my other small molecule. Are you >>>>>>>> sure that vdwradii.dat wont solve it while placing molecules using >>>>>>>> genbox and then solvating. The vdw radius of Fe(2+) is 2 A. Would you >>>>>>>> suggest something? >>>>>>>> >>>>>>> >>>>>>> Try it and see. If genbox doesn't find a radius, it uses a default >>>>>>> value, >>>>>>> which is specified with -vdwd on the command line, so modifications to >>>>>>> vdwradii.dat are not strictly necessary, but a more explicit command >>>>>>> might >>>>>>> be. >>>>>>> >>>>>>> -Justin >>>>> >>>>> >>>>> If change -vdwd to 0.2 it will affect slo water molecules which is not >>>>> desirable. Shall I just copy vdwradii.dat to my working directory and >>>>> add: >>>>> >>>>> >>>>> ??? FE 0.20 >>>>> >>>>> Will that change it? >>>>> >>>> >>>> Yes. >>>> >>>> -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 >>>> >>>> ======================================== >>>> -- >>>> 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 -- 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. 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