[gmx-users] GAFF and alkynes
Rebeca García Fandiño
regafan at hotmail.com
Thu Feb 12 15:43:50 CET 2015
Thanks a lot for the suggestions, Justin.
In your CO2 tutorial I have seen the comment "One cannot effectively build this
molecule in the traditional sense, as there are algorithmic reasons why
an angle of 180° is not stable during a simulation."
I was wondering what happens if I use angle restraints, for example. Would it lead to an unstable simulation? I suppose that if people use virtual sites to treat with linear molecules instead of applying angle restraints, there should be problems with this approximation...is this correct?
Rebeca
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
> From: gromacs.org_gmx-users-request at maillist.sys.kth.se
> Subject: gromacs.org_gmx-users Digest, Vol 130, Issue 35
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Date: Thu, 12 Feb 2015 14:56:03 +0100
>
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> Today's Topics:
>
> 1. Re: Gromacs's FTP site problems (Mark Abraham)
> 2. Re: Insertion of a carbon nanotube in a system (Justin Lemkul)
> 3. Re: GAFF and alkynes (Justin Lemkul)
> 4. Re: Effect of time step size (Justin Lemkul)
> 5. single strand DNA in hairpin conformation (Urszula Uciechowska)
> 6. Re: single strand DNA in hairpin conformation (Erik Marklund)
> 7. Re: Effect of time step size (Faezeh Pousaneh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Feb 2015 12:24:37 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Gromacs's FTP site problems
> Message-ID:
> <CAMNuMAS9js44NJd6aYS67GKRfDz0EXTsh__b-1k1RpWkdTecSg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Thanks for the query... It's worked fine for Justin Lemkul and me this
> morning.
>
> Mark
>
> On Thu, Feb 12, 2015 at 9:29 AM, Silvio a Beccara <abeccara at science.unitn.it
> > wrote:
>
> > Good morning,
> >
> > I've been trying to download a Gromacs tarball for a few days now, without
> > success.
> > It looks like Gromacs' FTP site is not working properly (I get the 550
> > Failed to change directory error).
> > Could anybody please check?
> >
> > Best regards
> >
> > Silvio a Beccara
> > --
> > 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
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> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 12 Feb 2015 07:44:00 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Insertion of a carbon nanotube in a system
> Message-ID: <54DCA010.8040205 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/11/15 11:29 PM, soumadwip ghosh wrote:
> > Dear users,
> > I am currently working in the direction of adsorption of
> > nucleic acids on the surface of single-wall carbon nanotubes (SWCNT) and I
> > have made a SWCNT with indices (3,3) using the package Tubegen. What I dont
> > know is how to insert it in my system containing nucleic acids, solvent and
> > ions. Is it possible to add the SWCNT just by making the topology by
> > altering the atom types with the help of pdb2gmx and then add it by using
> > -ci -nmol options of the genbox? Can I use packmole to generate the initial
> > structure by putting all the nucleic acis.PDB, SWCNT.PDB and spce.PDB
> > together? I saw a paper where the ssDNA-SWCNT has been modeled by using
> > xleap package of AMBER which I dont know how to use. Is there any other
> > simpler way for the above purpose? I hope I'm not asking for much.
> >
>
> Generate topologies for the nucleic acid and CNT independently; this will give
> you two topol.top files. Remove the system-level directives to make each of
> these an .itp file (see the wiki or manual). Create a new .top that #includes
> the parent force field, each of the nucleic acid and CNT .itp files, etc.
>
> Position the DNA and CNT in a suitable box using editconf independently (using
> rotation and translation options as needed to create the desired orientation),
> then concatenate the coordinate files. At this point, you'll have a CNT and DNA
> in a box, with no solvent. From here on, solvating, adding ions, etc. is the
> same as any simple system.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 12 Feb 2015 07:47:03 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GAFF and alkynes
> Message-ID: <54DCA0C7.5050009 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/12/15 4:40 AM, Rebeca Garc?a Fandi?o wrote:
> > Dear Gromacs users,
> > I am trying to simulate an organic molecule containing an alkyne, using GROMACS and the GAFF force field.
> > When I do grompp I get this note, referring to the atoms involved in the triple bond:
> >
> > NOTE 1 [file ligando_gmx.top, line 289]:
> > The bond in molecule-type solute between atoms 17 C12 and 18 C8 has an
> > estimated oscillational period of 1.7e-02 ps, which is less than 10 times
> > the time step of 2.0e-03 ps.
> > Maybe you forgot to change the constraints mdp option.
> >
> > The resulting structure from MD simulations is not correct, since the triple bonds should be linear (C-C=C-H), and I observe an angle among the atoms involved.
> >
> > Maybe GAFF is not well optimized for alkynes, or maybe the NOTE suggested by GROMACS is the responsible for this incorrect structure?
> >
>
> The bond vibration issue is separate from angles being represented property.
> Likely you're not dealing with the linear angle properly (i.e. not defining it
> correctly in the topology). Another approach is virtual site construction to
> define a linear moiety, as in my CO2 tutorial or as people have done for, e.g.
> acetonitrile (see the list archive).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 12 Feb 2015 07:49:46 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Effect of time step size
> Message-ID: <54DCA16A.3050203 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 2/12/15 4:58 AM, Faezeh Pousaneh wrote:
> > Dear Justin,
> >
> > Thank you. Yes, both correspond to same setting except dt.
> >
> > No, expected value is not known.
> >
> > I have just tried to re-simulate with different values of lincs_itr and
> > lincs_order (2 and 8 respectively) and I get similar values for densities.
> > Could that be a good solution?
> >
>
> In principle, you shouldn't have to do that in situations like these (note the
> descriptions of these options in the manual indicate only very specific cases
> should require increasing them beyond default). More likely, the agreement
> after these changes indicates that there was something unstable about the
> previous setup, such that the model is not producing reliable physics when you
> increase dt too much.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 12 Feb 2015 14:02:42 +0100
> From: "Urszula Uciechowska" <urszula.uciechowska at biotech.ug.edu.pl>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] single strand DNA in hairpin conformation
> Message-ID:
> <55c725912f3d5e878aa4b1bfa3f7918f.squirrel at poczta.ug.edu.pl>
> Content-Type: text/plain;charset=utf-8
>
> Hi gromacs users,
>
> Does anyone know how to build a ssDNA in hairpin conformation?
> Does anyone know maybe other free software where I could do this?
>
> Thank you in advance for any suggestions
>
> Best regards
> Urszula
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
> http://www.ug.edu.pl/
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 12 Feb 2015 13:26:25 +0000
> From: Erik Marklund <erik.marklund at chem.ox.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] single strand DNA in hairpin conformation
> Message-ID: <938C7319-81F8-4F97-BCB4-7030A9B8B8AA at chem.ox.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Ursula,
>
> Try macromolecular builder. It will require a bit of work, essentially building a helix with an unstructured loop that you relax according to a potential function.
>
> Kind regards,
> Erik
>
>
> Erik Marklund, PhD
> Postdoctoral Research Fellow, Fulford JRF
>
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>
> On 12 Feb 2015, at 13:02, Urszula Uciechowska <urszula.uciechowska at biotech.ug.edu.pl<mailto:urszula.uciechowska at biotech.ug.edu.pl>> wrote:
>
> Hi gromacs users,
>
> Does anyone know how to build a ssDNA in hairpin conformation?
> Does anyone know maybe other free software where I could do this?
>
> Thank you in advance for any suggestions
>
> Best regards
> Urszula
>
> University of Gdansk and Medical Univesity of Gdansk
> Department of Molecular and Cellular Biology
> ul. Kladki 24
> 80-822 Gdansk
> Poland
>
>
> -----------------------------------------
> Ta wiadomo?? zosta?a wys?ana z serwera Uniwersytetu Gda?skiego
> http://www.ug.edu.pl/
>
> --
> 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
>
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>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 12 Feb 2015 14:55:20 +0100
> From: Faezeh Pousaneh <fpoosaneh at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Effect of time step size
> Message-ID:
> <CAJtnTaW=51hU2v-SpOa6rSSOxD7rE1Be4NjHatMo_TCihX41cg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I see. thanks.
> Now can I continue simulations with the increased lincs values? or there is
> something wrong with my model and I should look for the source of
> unstability?
>
> Best regards
> *Faezeh Pousaneh*
>
> On Thu, Feb 12, 2015 at 1:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 2/12/15 4:58 AM, Faezeh Pousaneh wrote:
> >
> >> Dear Justin,
> >>
> >> Thank you. Yes, both correspond to same setting except dt.
> >>
> >> No, expected value is not known.
> >>
> >> I have just tried to re-simulate with different values of lincs_itr and
> >> lincs_order (2 and 8 respectively) and I get similar values for densities.
> >> Could that be a good solution?
> >>
> >>
> > In principle, you shouldn't have to do that in situations like these (note
> > the descriptions of these options in the manual indicate only very specific
> > cases should require increasing them beyond default). More likely, the
> > agreement after these changes indicates that there was something unstable
> > about the previous setup, such that the model is not producing reliable
> > physics when you increase dt too much.
> >
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > 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
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