noob noob wrote:
Dear all,.
I am quite new in MD simulations. I am planning to learn some simple
simulation, and now i encounter a little doubt about the bond
constraint. I get many references and papers to design a method for my
simulation but I cannot get a reference that use "no bond constraint" in
their works.
Hence, my question is:
Is it possible if we do not use bond constraint in our system?
Yes. You can set "constraints = none" in the .mdp file.
What is the different or effect if we do not use bond constraint compare
to those are using "all-bond "bond constraint?
is it wrong if we do not use bond constraint in our system?
It is not wrong, but it is quite advantageous to use constraints. If you don't,
you have to use a much smaller timestep and verify that energy is properly
conserved. Refer to the LINCS and P-LINCS papers (cited in the manual), and the
references therein.
-Justin
Thanks for any suggestions.
------------------------------------------------------------------------
Make the most of what you can do on your PC and the Web, just the way
you want. Windows Live <http://www.get.live.com/wl/all>
------------------------------------------------------------------------
_______________________________________________
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/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/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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/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/mailing_lists/users.php
