On Sat, 06 Sep 2008 06:13:35 -0400
"Justin A. Lemkul" <[EMAIL PROTECTED]> wrote:
Manoj Kumar Singh wrote:
What if I want to restrain distance between two different molecules. I
tried this and getting error. I looked at some previous posts and didn't
find any solution to this. Some of them say it is limitation of Gromacs.
Since distance restraints are added to the topology of one molecule, I
believe than can only be applied intramolecularly.
Justin is right, it has to be intramolecular, but you can merge the two
topologies in one and then add your distance restraint.
try: pdb2gmx -merge
-Justin
Is there any way I can put distance restraint between atoms of two
different molecules?
Thanks in advance!
Manoj
Manoj Kumar Singh wrote:
Hi,
I want to put distance based restrain between few pairs of atoms during
initial dynamics (along with Lincs on hbonds). I don't know how can I do
this.
Section 4.3.4 of the manual is probably a good start.
-Justin
I will highly appreciate any suggestion.
Manoj
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.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
Graduate Research Assistant
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://www.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
Graduate Research Assistant
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://www.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
-----------------------------------------------------
XAvier Periole - PhD
Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.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
