Yes, if you define it in a [ constraints ] directive, and use "constraints =
none" in your .mdp file, so that other bonds will not be converted to
constraints, but the one you explicitly set in the topology will be used.
-Justin
Nilesh Dhumal wrote:
Can I put constraint on selected bond?
Nilesh
On Sun, July 25, 2010 11:33 pm, Vitaly Chaban wrote:
1. Using freezegrps is not generally a good idea to fix a bond length.
Look at the constraints mechenism better. Or just try a bigger force
constant in topology.
2. NPT and freezegrps do not interact correctly, since freezegrps just
freezes any changes of atom positions, so they are not rescaled even if the
box size is changed in NPT.
3. Anyway, I think you have defined incorrect groups if your atoms of
interest are still movable. Check a diffusion constant of your bonded
atoms, it should be zero in the case of freezegrps.
Dr. Vitaly Chaban
I am trying to freeze a bond (3.5 A) in my system. I used the index
file to define group and I added this two lines in my .mdp file.
freezegrps = PA NE freezedim = Y Y Y Y Y Y
I used g_dist to verify the distance between the freezing atoms. During
the NVT simulation the distace is around 3.449 A and its constant
though out the simulation. For NPT simulation the distance varies from
3.449 to
3.1.
Can you tell why distance changes in NPT not in NVT.
How can I freeze a bond om NPT simulation?
--
gmx-users mailing list [email protected]
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 [email protected]. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
