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? Steven >> >> >> -- >> ======================================== >> >> 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
