On 11/04/2012 1:24 AM, Shi, Huilin wrote:
Hi All,
I have a question about periodic boundary conditions (pbc) when
running a simulation to unfold a protein from its native structure.
I set up pbc with the starting structure which is compact.
When defining the box we use editconf and set up the -d 1.0 as the
distance from the protein to the box edge.
It is said that "a protein should never see its periodic image".
If during the simulation the protein starts unfolding, the minimum
distance from the protein to the box edge will no longer be 1.0 nm.
And it is possible that the length of the protein is even longer than
the box dimension and the protein may "see" its periodic image in the
neighbored box.
Is this going to be a problem?
Yes, if you don't allow for it from the start. Some test simulations
with implicit solvent are probably priceless here.
I am also confused that it is also said that "(parts of) the
molecule(s) diffuse out of the box is not a problem".
Is this conflicted with "a protein should never see its periodic image"?
Sometimes - can depend on orientation of molecule wrt box.
Mark
--
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
