[gmx-users] selecting atoms in index file

G R golnaz.chem at gmail.com
Thu Sep 7 14:03:11 CEST 2017


On Thu, Sep 7, 2017 at 12:35 PM, <
gromacs.org_gmx-users-request at 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.Hermann at lrz.tu-muenchen.de>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] selecting atoms in index file
> Message-ID: <c1fd2b6b-91f9-5ec7-d39d-4b666599a226 at 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.hermann at lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 7 Sep 2017 11:18:29 +0200
> From: "Hermann, Johannes" <J.Hermann at lrz.tu-muenchen.de>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] DPOSRES not working
> Message-ID: <8c01673e-77d8-fa16-c5ad-ec0269a4752e at 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 = 10000000
> > 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
> >
> > Sergio Manzetti
> >
> > [ http://www.fjordforsk.no/logo_hr2.jpg ]
> >
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [
> http://www.fjordforsk.no/ |   ]
> > Midtun
> > 6894 Vangsnes
> > Norge
> > Org.nr. 911 659 654
> > Tlf: +47 57695621
> > [ http://www.oekolab.com/ | ?kolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
> >
>
> --
> ______________________________________
> *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.hermann at lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 7 Sep 2017 11:15:40 +0200 (CEST)
> From: Sergio Manzetti <sergio.manzetti at fjordforsk.no>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] DPOSRES not working
> Message-ID:
>         <261160509.13922159.1504775740212.JavaMail.zimbra at fjordforsk.no>
> Content-Type: text/plain; charset=utf-8
>
> Hi Johannes, it appears so:
>
>
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_DNA_chain_E.itp"
> #include "topol_DNA_chain_F.itp"
> #include "PRB_GMX.itp"
>
> ; Include water topology
> #include "amber99sb-ildn.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
>
> [ system ]
> ; Name
> CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water
>
> [ molecules ]
> ; Compound #mols
> DNA_chain_E 1
> DNA_chain_F 1
> NA 71
> CL 31
> PRB 1
> SOL 16349
>
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | ?kolab? ] | [ http://www.nanofact.no/ |
> Nanofactory? ] | [ http://www.aq-lab.no/ | AQ-Lab? ] | [
> http://www.phap.no/ | FAP ]
>
>
>
> From: "Hermann, Johannes" <J.Hermann at lrz.tu-muenchen.de>
> To: "gmx-users" <gmx-users at gromacs.org>
> Sent: Thursday, September 7, 2017 11:18:29 AM
> Subject: Re: [gmx-users] DPOSRES not working
>
> 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 = 10000000
> > 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
> >
> > Sergio Manzetti
> >
> > [ http://www.fjordforsk.no/logo_hr2.jpg ]
> >
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [
> http://www.fjordforsk.no/ | ]
> > Midtun
> > 6894 Vangsnes
> > Norge
> > Org.nr. 911 659 654
> > Tlf: +47 57695621
> > [ http://www.oekolab.com/ | ?kolab ] | [ http://www.nanofact.no/ |
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/
> | FAP ]
> >
>
> --
> ______________________________________
> *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.hermann at lrz.tum.de
> http://www.biovt.mw.tum.de/
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 7 Sep 2017 11:29:03 +0200
> From: "Hermann, Johannes" <J.Hermann at lrz.tu-muenchen.de>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] DPOSRES not working
> Message-ID: <fd2d6827-1c92-a8b4-aeff-4931612b01b8 at lrz.tum.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Okay, but what did you define in your topologies for your DNA chains:
>
> #include "topol_DNA_chain_E.itp"
> #include "topol_DNA_chain_F.itp"
>
> Make sure that at the end of these files you have lines stating e.g:
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_DNA_chain_E.itp"
> #endif
>
> The same for your other chain.
>
> Normally pdb2gmx creats a position restrain file posre_DNA_chain_E.itp
> for all the heavy atoms. If you do not have this position restrain file
> you can generate it with gmx genrestr.
>
> Last but not least you can read about position restrains in the manual.
>
> All the best
> Johannes
>
>
> On 07.09.2017 11:15, Sergio Manzetti wrote:
> > Hi Johannes, it appears so:
> >
> >
> > ; Include forcefield parameters
> > #include "amber99sb-ildn.ff/forcefield.itp"
> >
> > ; Include chain topologies
> > #include "topol_DNA_chain_E.itp"
> > #include "topol_DNA_chain_F.itp"
> > #include "PRB_GMX.itp"
> >
> > ; Include water topology
> > #include "amber99sb-ildn.ff/spc.itp"
> >
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ; i funct fcx fcy fcz
> > 1 1 1000 1000 1000
> > #endif
> >
> > ; Include topology for ions
> > #include "amber99sb-ildn.ff/ions.itp"
> >
> > [ system ]
> > ; Name
> > CRYSTAL STRUCTURE OF P53 CORE DOMAIN IN COMPLEX WITH DNA in water
> >
> > [ molecules ]
> > ; Compound #mols
> > DNA_chain_E 1
> > DNA_chain_F 1
> > NA 71
> > CL 31
> > PRB 1
> > SOL 16349
> >
> >
> >
> > Sergio Manzetti
> >
> > [ http://www.fjordforsk.no/logo_hr2.jpg ]
> >
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [
> http://www.fjordforsk.no/ |   ]
> > Midtun
> > 6894 Vangsnes
> > Norge
> > Org.nr. 911 659 654
> > Tlf: +47 57695621
> > [ http://www.oekolab.com/ | ?kolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
> >
> >
> >
> > From: "Hermann, Johannes" <J.Hermann at lrz.tu-muenchen.de>
> > To: "gmx-users" <gmx-users at gromacs.org>
> > Sent: Thursday, September 7, 2017 11:18:29 AM
> > Subject: Re: [gmx-users] DPOSRES not working
> >
> > 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 = 10000000
> >> 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
> >>
> >> Sergio Manzetti
> >>
> >> [ http://www.fjordforsk.no/logo_hr2.jpg ]
> >>
> >> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [
> http://www.fjordforsk.no/ | ]
> >> Midtun
> >> 6894 Vangsnes
> >> Norge
> >> Org.nr. 911 659 654
> >> Tlf: +47 57695621
> >> [ http://www.oekolab.com/ | ?kolab ] | [ http://www.nanofact.no/ |
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/
> | FAP ]
> >>
>
> --
> ______________________________________
> *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.hermann at lrz.tum.de
> http://www.biovt.mw.tum.de/
>
>
>
> Email: j.hermann at lrz.tum.de
> http://www.biovt.mw.tum.de/
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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>
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> ******************************************************
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