vivek sharma wrote:
Hi justin,
My apologies for asking you so many small queries.
Can you suggest any good tutorial or reference that talks about this
issue of running MD over a selected part of molecule.
If you're using PR, all you're doing is position-restrained dynamics.
-Justin
With Thanks,
Vivek
2008/10/10 vivek sharma <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
hI justin,
Thanks for your response.
do I need to specify the index file(for residue that I want to keep
fix during MD) during GROMPP or just including the psre.itp in
topology is enough for the purpose ?
With Thanks,
Vivek
2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Justin A. Lemkul wrote:
vivek sharma wrote:
Thanks Justin,
My goal is to keep certain part fixed and move only a
few of the residues (case is like providing flexibility
to the site of interest only).
SO , do I need to specify the residue using some index
file ?
or is there some other way to specify the part of
molecule for position restraining ??
Make an index file with the residues you want to keep fixed, and
pass it
to genpr to generate a new posre.itp that corresponds to those
residues.
-Justin
With Thanks,
Vivek
2008/10/10 Justin A. Lemkul <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>
vivek sharma wrote:
Hi there,
I want to run MD over a part of my molecule ,
for few residues
only (not the whole molecule).
Can I do it using GROMACS ?
I searched for the online documentation and
mailing list, but
unable to get appropriate information.
If somebody has already tried such things
earlier, please
suggest and direct me for appropriate link and
address.
Well, if your goal is to keep certain parts fixed and
allow others
to move, probably the easiest way to do it is to
apply position
restraints to the "fixed" part.
-Justin
With Thanks,
Vivek
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto: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]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[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 <http://vt.edu> <http://vt.edu> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto: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]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
<mailto: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]
<mailto:[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
