[gmx-users] Protein from the line chain
s.neumann08 at gmail.com
Fri Aug 3 16:47:48 CEST 2012
On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul <jalemkul at vt.edu> 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.
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.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> * 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 gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users