[gmx-users] clayff forcefield
G R
golnaz.chem at gmail.com
Tue Aug 8 08:37:14 CEST 2017
On Tue, Aug 8, 2017 at 12:00 AM, <
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> 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 <holyriver6 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] solvate only in the z-direction
> Message-ID:
> <CAE2xNzam5N=cR=0yh4V_yhWhNpD=aa+kwde-X+=OzFp-MeE1EA at 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.chem at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] clayff forcefield
> Message-ID:
> <CAGFO7SH0Q4EycB+A=hh2WThN219H6gmeHgE3rq87xguDnGsM4A at 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.abraham at gmail.com>
> To: gmx-users at 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 <maghesree.c at 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.abraham at 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 <maghesree.c at 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
> > > >
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> > > --
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>
> ------------------------------
> 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.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] clayff forcefield
> Message-ID:
> <CAMNuMARHLA9+6rBRR1wzmiaiyz_5oU9QLx3urvbvfQ4LZTn50w at 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.chem at 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 07 Aug 2017 20:58:25 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] clayff forcefield
> Message-ID:
> <CAMNuMARHLA9+6rBRR1wzmiaiyz_5oU9QLx3urvbvfQ4LZTn50w at 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.chem at 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 07 Aug 2017 21:00:03 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] solvate only in the z-direction
> Message-ID:
> <CAMNuMARV3EzRX0fkObQnWTgp9SZ76QgmKUFNdP74druLZZB+BQ at 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 <holyriver6 at 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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