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 <[email protected]> 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 <[email protected]> wrote: >> :)))))))))))) >> >> On Thu, Nov 15, 2012 at 2:58 PM, Justin Lemkul <[email protected]> wrote: >>> >>> >>> On 11/15/12 9:57 AM, Steven Neumann wrote: >>>> >>>> On Thu, Nov 15, 2012 at 2:35 PM, Steven Neumann <[email protected]> >>>> wrote: >>>>> >>>>> I will. Thank you. >>>>> >>>>> Steven >>>>> >>>>> On Thu, Nov 15, 2012 at 2:30 PM, Justin Lemkul <[email protected]> wrote: >>>>>> >>>>>> >>>>>> >>>>>> On 11/15/12 9:03 AM, Steven Neumann wrote: >>>>>>> >>>>>>> >>>>>>> On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul <[email protected]> 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 [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 -- 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? 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