On Thu, Sep 7, 2017 at 12:35 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
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> Today's Topics:
>
>1. Re: selecting atoms in index file (Hermann, Johannes)
>2. Re: DPOSRES not working (Hermann, Johannes)
>3. Re: DPOSRES not working (Sergio Manzetti)
>4. Re: DPOSRES not working (Hermann, Johannes)
>5. Re: DPOSRES not working (Sergio Manzetti)
>
>
> --
>
> Message: 1
> Date: Thu, 7 Sep 2017 11:16:08 +0200
> From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] selecting atoms in index file
> Message-ID: <c1fd2b6b-91f9-5ec7-d39d-4b666599a...@lrz.tum.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Golnaz,
>
> do you know the number (index) of the respective atoms? E.g. open the
> .gro file in vmd and look for the atoms?
>
> If there are not too many atoms, you can manually edit your index file.
> E.g. create a default index file (gmx make_ndx) and add the subset of
> indexes with a new selection definition:
>
> ---
>
> [ MySelection]
>
> 23 57 75
>
> ---
>
> All the best
>
> Johannes
>
> Hi Johanne,
>
> Thank you for your reply. just one more question: when I edit atoms in my
> index file, should I delete these atoms from surfaces groups. let me
> explain better. Now I have 2 groups in my index file Sol and
> Kaoli(surface). I should select some atoms from the Kaoli. So first I
> define the atoms that I want to select in a seperate group, then I should
> erase these atoms from kaoli parts. Am I right? because I want to freeze
> the surface without these atoms.
>
> On 07.09.2017 11:02, G R wrote:
> > Dear All,
> >
> > I want to create an index file and select some especial atoms in a
> surface.
> > My problem is that I have only one residue for the whole surface. How
> can I
> > select the atoms on the surface as a different groups in my index file?
> >
> > Thank you in advance,
> > Golnaz
>
> --
> __
> *Technische Universit?t M?nchen*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl f?r Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
>
> --
>
> Message: 2
> Date: Thu, 7 Sep 2017 11:18:29 +0200
> From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] DPOSRES not working
> Message-ID: <8c01673e-77d8-fa16-c5ad-ec0269a47...@lrz.tum.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Sergio,
>
> how did you define the position restrain in your topology? Check your
> topology and position restrain file.
>
> All the best
>
> Johannes
>
>
> On 07.09.2017 11:07, Sergio Manzetti wrote:
> > Hello, I am running 5 simulations with the given mdp:
> >
> > title = DNA in water stabilization
> > cpp = /lib/cpp
> > include = -I../top
> > define = -DPOSRES
> > integrator = md
> > dt = 0.002
> > nsteps = 1000
> > nstxout = 5000
> > nstvout = 5000
> > nstlog = 5000
> > nstenergy = 300
> > nstxout-compressed = 300
> > compressed-x-grps = PRB SOL NA CL DNA
> > energygrps = PRB SOL NA CL DNA
> > nstlist = 10
> > ns-type = grid
> > rlist = 0.8
> > coulombtype = PME
> > rcoulomb = 0.8
> > rvdw = 0.8
> > tcoupl = V-Rescale
> > tc-grps = System
> > tau-t = 0.1
> > ref-t = 310
> > Pcoupl = No
> > tau-p = 1.0
> > compressibility = 4.5e-5
> > ref-p = 1.0
> > gen-vel = yes
> > gen-temp = 310
> > gen-seed = 17527
> > constraints = all-bonds
> >
> >
> > and still, the DNA splits into two
> >
> > Any ideas what could be wrong?
> >
> > Thanks
> &
