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? Read http://www.gromacs.org/Support/Mailing_Lists
