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
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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