:))))))))))))
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
