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 > > > -- > ======================================== > > 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
