On 2/22/13 4:37 AM, Mehdi Bagherpour wrote:
Tanks Justin
Should I use from 'define = -DPOSRES' in mdp file?
Use whatever #ifdef construct makes sense. The -DPOSRES uses the default
posre.itp written by pdb2gmx, which restrains all heavy atoms. Unless you've
modified the topology, that approach will not use your special restraint file.
-Justin
On Fri, Feb 22, 2013 at 4:13 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/21/13 7:35 PM, Mehdi Bagherpour wrote:
Thanks Justin
I have any question?
i will use minimization with this restrain.
using genrestr I make min.itp.
how should I use this .itp file in grompp or mdrun?
As you would any other .itp file; #include it in the topology, within the
corresponding [moleculetype].
-Justin
On Fri, Feb 22, 2013 at 2:41 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/21/13 6:09 PM, Mehdi Bagherpour wrote:
I am using Gromacs software for DNA simulation. Specially in my project
I
need to fix two ends base pairs of DNA,The DNA that I want to simulate
has
12 sequence shown bellow
5-- *C*GCAAAAAACG*C* --3
3-- *G*CGTTTTTTGC*G* --5
I dont know how I can use from position restraint in gromacs.
would you please help me to solve this problem?
Use genrestr with an index group specifying whatever it is that you
want
to restrain.
-Justin
--
==============================****==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
<h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<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<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
<htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
Mailing_Lists/Search<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<http://www.gromacs.org/**Support/Mailing_Lists>
<http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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
