On Thu, Sep 7, 2017 at 12:35 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > 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 = 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.herm...@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.manze...@fjordforsk.no> > To: gmx-users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] DPOSRES not working > Message-ID: > <261160509.13922159.1504775740212.javamail.zim...@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.herm...@lrz.tu-muenchen.de> > To: "gmx-users" <gmx-us...@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.herm...@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-requ...@gromacs.org. > > > ------------------------------ > > Message: 4 > Date: Thu, 7 Sep 2017 11:29:03 +0200 > From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] DPOSRES not working > Message-ID: <fd2d6827-1c92-a8b4-aeff-4931612b0...@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.herm...@lrz.tu-muenchen.de> > > To: "gmx-users" <gmx-us...@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.herm...@lrz.tum.de > http://www.biovt.mw.tum.de/ > > > > Email: j.herm...@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-requ...@gromacs.org. > > > ------------------------------ > > -- > 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-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 161, Issue 16 > ****************************************************** > -- 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-requ...@gromacs.org.