On Tue, Aug 8, 2017 at 12:00 AM, < 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. solvate only in the z-direction (gangotri dey) > 2. clayff forcefield (G R) > 3. Re: Constraining starting configuration in Coarse-Grain > Simulation (Mark Abraham) > 4. Re: clayff forcefield (Mark Abraham) > 5. Re: clayff forcefield (Mark Abraham) > 6. Re: solvate only in the z-direction (Mark Abraham) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 7 Aug 2017 16:32:42 -0400 > From: gangotri dey <holyriv...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] solvate only in the z-direction > Message-ID: > <CAE2xNzam5N=cR=0yh4V_yhWhNpD=aa+kwde-X+=OzFp-MeE1EA@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > > I am working with MnO2 surface and I would like to solvate the surface only > in the z-direction. How best can I do it, please? > > *Thank you* > > *Gangotri Dey* > > > ------------------------------ > > Message: 2 > Date: Mon, 7 Aug 2017 23:53:37 +0300 > From: G R <golnaz.c...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] clayff forcefield > Message-ID: > <CAGFO7SH0Q4EycB+A=hh2WThN219H6gmeHgE3rq87xguDnGsM4A@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear usres, > > I try to write clayff forcefield, and I want to simulate Kaolinite. I have > some questions about it. > 1) should I write clayff forcefield separately or modify one of the > forcefields in share/top? > 2) The directory for clayff forcefield should be included ffbonded.itp, > ffnonbonded.itp, atomname2type.n2t, forcefield.itp, > forcefield.doc,atomtype.atp? if it is needed any other file please let me > know? > 3) In .n2t file, the first column should be written corresponding .gro > file? > 4) For Kaolinite I only have two type of Oxygen, ob (bridging oxygen) and > oh (oxygen in hydroxyl group). Am I right? > > Any help will be appreciated, > Golnaz > > > ------------------------------ > > Message: 3 > Date: Mon, 07 Aug 2017 20:56:56 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Constraining starting configuration in > Coarse-Grain Simulation > Message-ID: > <CAMNuMARQMC1sCkkOhaXR_2ti23r2HS_86Z8DSdJrS06XEtV5oA@ > mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > Ok, I didn't understand you because I didn't have enough information yet. > IIRC your topology will still have to specify the constraint bond length, > you can't have grompp infer it from the starting coordinates. You should > also get a single molecule working correctly, because the symptoms of > broken topology and broken initial coordinates are often not > distinguishable. Prove the topology first when there cannot be an > inter-molecular clash. > > Mark > > On Mon, 7 Aug 2017 22:00 Maghesree Chakraborty <maghesre...@gmail.com> > wrote: > > > Thank you for your response. I did not have tabulated potentials for > bonded > > interactions. I had tabulated potentials only for non-bonded > > interactions. I had set constraints to be all-angles in my mdp file. I > will > > try using "constraint" interaction explicitly in my topology instead of > > converting bonds and angles into constraints via mdp directive. > > > > On Mon, Aug 7, 2017 at 1:58 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > > > Hi, > > > > > > Tabulated bonded interactions are the opposite of constraints. You can > > > explicitly use a "constraint" interaction type in your topology, which > > > sounds like a good start. See chapter five of the reference manual. > > > > > > Mark > > > > > > On Mon, 7 Aug 2017 01:24 Maghesree Chakraborty <maghesre...@gmail.com> > > > wrote: > > > > > > > Hello, > > > > > > > > I am trying to run a CG simulation with only non-bonded > interactions. I > > > > have obtained the tabulated potentials for those interactions by > > > > force-matching using VOTCA. I want all my bonds and angles to be > > > > constrained as they are in the initial cg_conf.gro file. Since I do > not > > > > have tabulated potentials for bonded interactions, gromacs gives > error > > > if I > > > > do not provide the bond and angle parameters (b0,kb and ?0 , k?) in > the > > > > topology file. Then I tried setting the bond parameter (b0) to be the > > > mean > > > > of bond-length distribution in cg_conf.gro and the angle parameter > (?0) > > > to > > > > be the mean of the angle distribution in cg_conf.gro, I constrain the > > > bonds > > > > and angles with LINCS in my grompp file. During simulation, I get a > lot > > > of > > > > LINCS warning and simulation is aborted. I am wondering if there is a > > way > > > > of constraining the initial configurations of the molecules as they > are > > > in > > > > cg_conf.gro file in the absence of tabulated bonded potentials and > not > > > > forcing the molecules to have the bond-lengths and angles as > specified > > > by > > > > the topology parameters. > > > > > > > > Thank you. > > > > > > > > Regards, > > > > M. Chakraborty > > > > -- > > > > 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. > > -- > > 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. > > > ------------------------------ > Hi, > Thank you for your answer. yes, I know that I should make my own forcefield in my working directory, and I made this forcefield, but when I use x2top to generate itp file, gromacs could not find my own forcefield (I named the forcefield file clayff.ff) in my working directory. Gromacs use the oplsaa in the share/top file instead, and obviusly the itp file doesn't generate. So, I asked again to be sure about my procedure. In my last project I modified oplsaa for generating itp file for graphen and I did not have this problem. Gromacs could easily recognize the forcefiled file in current directory, but in clayff case I can't understand why it read forcefield in shar/top instead of in current directory! > Message: 4 > Date: Mon, 07 Aug 2017 20:58:25 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] clayff forcefield > Message-ID: > <CAMNuMARHLA9+6rBRR1wzmiaiyz_5oU9QLx3urvbvfQ4LZTn50w@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > Didn't someone already answer that you need to make a forcefield folder, eg > in your working directory? You will need to follow the examples in the > gromacs version you are using to name things appropriately. > > Mark > > On Mon, 7 Aug 2017 22:54 G R <golnaz.c...@gmail.com> wrote: > > > Dear usres, > > > > I try to write clayff forcefield, and I want to simulate Kaolinite. I > have > > some questions about it. > > 1) should I write clayff forcefield separately or modify one of the > > forcefields in share/top? > > 2) The directory for clayff forcefield should be included ffbonded.itp, > > ffnonbonded.itp, atomname2type.n2t, forcefield.itp, > > forcefield.doc,atomtype.atp? if it is needed any other file please let me > > know? > > 3) In .n2t file, the first column should be written corresponding .gro > > file? > > 4) For Kaolinite I only have two type of Oxygen, ob (bridging oxygen) and > > oh (oxygen in hydroxyl group). Am I right? > > > > Any help will be appreciated, > > Golnaz > > -- > > 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: 5 > Date: Mon, 07 Aug 2017 20:58:25 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] clayff forcefield > Message-ID: > <CAMNuMARHLA9+6rBRR1wzmiaiyz_5oU9QLx3urvbvfQ4LZTn50w@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > Didn't someone already answer that you need to make a forcefield folder, eg > in your working directory? You will need to follow the examples in the > gromacs version you are using to name things appropriately. > > Mark > > On Mon, 7 Aug 2017 22:54 G R <golnaz.c...@gmail.com> wrote: > > > Dear usres, > > > > I try to write clayff forcefield, and I want to simulate Kaolinite. I > have > > some questions about it. > > 1) should I write clayff forcefield separately or modify one of the > > forcefields in share/top? > > 2) The directory for clayff forcefield should be included ffbonded.itp, > > ffnonbonded.itp, atomname2type.n2t, forcefield.itp, > > forcefield.doc,atomtype.atp? if it is needed any other file please let me > > know? > > 3) In .n2t file, the first column should be written corresponding .gro > > file? > > 4) For Kaolinite I only have two type of Oxygen, ob (bridging oxygen) and > > oh (oxygen in hydroxyl group). Am I right? > > > > Any help will be appreciated, > > Golnaz > > -- > > 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: 6 > Date: Mon, 07 Aug 2017 21:00:03 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] solvate only in the z-direction > Message-ID: > <CAMNuMARV3EzRX0fkObQnWTgp9SZ76QgmKUFNdP74druLZZB+BQ@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Solvate everything and then delete all molecules that have any > inappropriate z coordinate. Or make a box whose lowest z coordinate is what > you want, solvate that, and then add your surface below that. > > Mark > > On Mon, 7 Aug 2017 22:33 gangotri dey <holyriv...@gmail.com> wrote: > > > Dear all, > > > > I am working with MnO2 surface and I would like to solvate the surface > only > > in the z-direction. How best can I do it, please? > > > > *Thank you* > > > > *Gangotri Dey* > > -- > > 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 160, Issue 42 > ****************************************************** > -- 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.