Re: [gmx-users] position restrain of DNA

2013-02-22 Thread Justin Lemkul
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

Re: [gmx-users] position restrain of DNA

2013-02-22 Thread Mehdi Bagherpour
Tanks Justin Should I use from 'define = -DPOSRES' in mdp file? On Fri, Feb 22, 2013 at 4:13 AM, Justin Lemkul 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 m

Re: [gmx-users] position restrain of DNA

2013-02-21 Thread Justin Lemkul
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 corres

Re: [gmx-users] position restrain of DNA

2013-02-21 Thread Mehdi Bagherpour
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? On Fri, Feb 22, 2013 at 2:41 AM, Justin Lemkul wrote: > > > On 2/21/13 6:09 PM, Mehdi Bagherpour wrote: > >> I am using Gromacs

Re: [gmx-users] position restrain of DNA

2013-02-21 Thread Justin Lemkul
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*GCAACG*C* --3 3-- *G*CGTTGC*G* --5 I dont know how I can us