On Fri, Aug 3, 2012 at 3:51 PM, Justin Lemkul <[email protected]> wrote: > > > On 8/3/12 10:47 AM, Steven Neumann wrote: >> >> On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul <[email protected]> wrote: >>> >>> >>> >>> On 8/3/12 10:27 AM, Steven Neumann wrote: >>>> >>>> >>>> Dear Gmx Users, >>>> >>>> I want to simulate protein line chain (80 residues) in explicit >>>> sovent. Let's assume its axis is x direction. What should be the z and >>>> y dimension of the box? Is there any rule? Would you wait e.g. for 50 >>> >>> >>> >>> The box size in all dimensions needs to be sufficient to accommodate the >>> protein chain in a fully extended configuration aligned with any axis. >>> You >>> can't predict how the protein will rotate, and it is possible (though >>> probably unlikely) to rotate 90 degrees in any direction without >>> collapsing >>> at all. A dodecahedral box is your friend here, but a huge amount of >>> atoms >>> is unavoidable. >>> >>> >>>> ns when it folds and then decrease the simulation box? >>>> >>> >>> In doing so, you have to justify your results in the context of a >>> discontinuous series of simulations. Implicit solvent may be a much more >>> advantageous approach. >>> >>> -Justin >> >> >> >> Thank you. What do you mean by discontinuous series of simulations? I >> have to use explicit solvent unfortunately. Once it folds in a huge >> box I can stop it and place it into the smaller one. >> > > Precisely - you run one simulation, obtain a configuration (is it > representative of the first part of the simulation? randomly chosen?) and > re-solvate it such that hydration is disrupted unless you take care to > extract a solvation shell around the protein. Even then, you can't preserve > the previous state with respect to thermodynamic observables so it's > basically a new simulation from some arbitrarily chosen configuration. If > you're studying protein folding, that can seem a bit fishy. In principle, > there's nothing immediately wrong with doing this, but always be prepared to > justify your approach. There are a lot of very tricky questions a reviewer > can ask if care is not taken. > > -Justin >
Thank you Justin for the clear explanation. 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 > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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
