Frank Neuhaus wrote:
Hi,
I have a protein simulation in which all residues simulate correctly
with the exception of five in a loop. These five out of 360 are in a
loop (or bend) separate from my area of interest. Thus, I would like to
treat them as a rigid sequence. Using the position restraints in the
posre.itp file does not help me. I am looking for a script that I can
write into my mdp files that restricts all simulation in these five
residues. Can anyone help me with this little issue? Thank you.
You can use freezegrps to completely prevent any changes to the coordinates.
Whether or not this makes any physical sense or will have any artifactual
influence on the rest of your protein is up to you to decide. Note that (if I
recall correctly), you cannot use an NPT ensemble when applying freezegrps due
to the coordinate scaling intrinsic to the barostat algorithms.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
