[gmx-users] gromacs.org_gmx-users Digest, Vol 173, Issue 84

Fri Sep 21 18:42:25 CEST 2018

Hi,

What do you mean by atom selection and how do I do that  ?

By using gmx clustersize we can get the index file containing the atom
numbers of the largest cluster.  How can I get index file of all other
aggregates in the system.

Aishwarya

On Fri, Sep 21, 2018 at 3:08 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Re: GROMACS user workshop (Benson Muite)
>    2. Re: protein dna pulling (Erik Marklund)
>    3. Re: Nonbonded energy of 1-4 interactions (Zhonghua Xia)
>    4. Re: Nonbonded energy of 1-4 interactions (Justin Lemkul)
>    5. Aggregation Analysis (Aishwarya Dhar)
>    6. Aggregation Analysis (Aishwarya Dhar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 Sep 2018 13:40:09 +0300
> From: Benson Muite <benson.muite at ut.ee>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] GROMACS user workshop
> Message-ID: <c9d9718b-5539-0590-41c8-ebb9a2f6a347 at ut.ee>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
> 1) There is a possibility to apply for funding support to attend the
> workshop - the earlier you do this, the better. Workshop attendance is
> free, though registration is required. Note that the cost of
> accommodation in Riga is significantly lower than many other European
> cities. Latvia is part of the Schengen zone.
>
> 2) Language of instruction at the workshop will be English. Some
> workshop participants may also use other languages in informal discussion.
>
> 3) The workshop will be suitable for those with limited GROMACS
> experience (motivated undergraduate students with introductory science
> and programming background should be able to learn how to use GROMACS).
> The hands on sessions will be more attendee driven than the lectures,
> with a mix of introductory topics and more specialized material.
>
> On 09/21/2018 07:27 AM, Benson Muite wrote:
> > Hi,
> >
> > Thanks for the suggestion. This depends on speaker willingness to be
> > recorded.
> >
> > Benson
> >
> > On 09/21/2018 05:52 AM, T?ng Ho?ng wrote:
> >> i hope have youtube link for people around the world could learn it
> >>
> >> V?o Th 4, 19 thg 9, 2018 va?o lu?c 21:13 Benson Muite <
> benson.muite at ut.ee>
> >> ?? vi?t:
> >>
> >>> Hi,
> >>>
> >>> There will be a GROMACS user workshop in Riga, Latvia on Friday 26 and
> >>> Saturday 27 October. Some more information is available at:
> >>> https://baltichpc.org/
> >>>
> >>> Best wishes,
> >>> Benson
> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 21 Sep 2018 11:45:45 +0000
> From: Erik Marklund <erik.marklund at kemi.uu.se>
> To: "<gmx-users at gromacs.org> GROMACS users" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] protein dna pulling
> Message-ID: <EA2050C5-53D6-4099-8EB3-D3A7D5819346 at kemi.uu.se>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> Not necessarily. The COM still moves if one strand moves away. Your
> results however suggest that the DNA?s interaction with the protein is
> stronger than the interaction between strands. I will leave it up to you to
> decide whether that makes sense or not, or if there is something wrong with
> your setup.
>
> Kind regards,
> Erik
> ______________________________________________
> Erik Marklund, PhD, Marie Sk?odowska Curie INCA Fellow
> Department of Chemistry ? BMC, Uppsala University
> +46 (0)18 471 4542
> erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>
>
> On 27 Aug 2018, at 20:11, abhisek Mondal <abhisek.mndl at gmail.com<mailto:
> abhisek.mndl at gmail.com>> wrote:
>
> Hi,
> I have been trying to pull a double stranded DNA from protein's binding
> surface. But I am facing an issue. After defining the pull vector when I
> apply the pull force the DNA's one stand got pulled completely while other
> strand partially remain attached (
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaG
> psUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
> ).
> Shouldn't the both strands be moving together (as the COM was determined
> using residues from both strand of DNA) ?
> Some suggestions in this regard would be highly appreciated.
> Thank you.
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
> *Protein Crystallography Group*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
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>
>
>
>
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> ------------------------------
>
> Message: 3
> Date: Fri, 21 Sep 2018 14:25:32 +0200
> From: Zhonghua Xia <zhonghua.xia at helmholtz-muenchen.de>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Nonbonded energy of 1-4 interactions
> Message-ID:
>         <DDDBFFF1-8697-4F3C-8DB3-5CF42248693E at helmholtz-muenchen.de>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Justin,
>
> Thank you so much for your answer!
>
> So, if I want to calculate the nonbonded energy of solute-solute and
> solute-solvent, I should set the parameter as below:
>
> energygrps = MOL MOL MOL SOL
>
> And If I want to customise FudgeLJ and FudgeQQ, is it feasible to directly
> modify their values in the forcefield.itp file?
>
> Kind regards,
> Zhonghua
>
>
>
> On 9/20/18 5:23 AM, Zhonghua Xia wrote:
> > Dear all,
> >
> > I want to get the nonbonded energy (1-4 electrostatic and 1-4 LJ) of
> solute-solute and solute-solvent, respectively. How can I make it? What?s
> more, how can I set the scaling-factors of them?
>
> These energies are in LJ-14 and Coul-14 in the .edr file. If you want
> them decomposed for different groups, you need to specify energygrps in
> the .mdp file, re-create a .tpr file with those groups, and post-process
> your trajectory. Note that 1-4 interactions are intramolecular, so there
> is no such thing as a solute-solvent 1-4 energy. The term also has no
> physical meaning as it is completely dependent upon force field
> convention and dihedral terms.
>
> In GROMACS, the 1-4 scaling factors are set with FudgeLJ and FudgeQQ in
> the [defaults] directive of forcefield.itp.
>
> -Justin
>
> ------------------------------
>
> Message: 4
> Date: Fri, 21 Sep 2018 08:40:48 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Nonbonded energy of 1-4 interactions
> Message-ID: <c7fc0460-812f-ec67-8f9b-277ce31b1138 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/21/18 8:25 AM, Zhonghua Xia wrote:
> > Hi Justin,
> >
> > Thank you so much for your answer!
> >
> > So, if I want to calculate the nonbonded energy of solute-solute and
> solute-solvent, I should set the parameter as below:
> >
> > energygrps = MOL MOL MOL SOL
>
> No, just energygrps = MOL SOL
>
> mdrun builds the matrix from the listed groups. Again, be aware that for
> most force fields, this quantity has no physical meaning.
>
> > And If I want to customise FudgeLJ and FudgeQQ, is it feasible to
> directly modify their values in the forcefield.itp file?
>
> You can modify it, but then you break the force field convention because
> you invalidate all the dihedral parameters, which require a given 1-4
> scaling to be balanced.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 21 Sep 2018 15:00:56 +0200
> From: Aishwarya Dhar <dhar.aishwarya at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Aggregation Analysis
> Message-ID:
>         <CAEod-am+FJTDCXp_LbMoqd2A4szH_WP5HGcnbrR2CoszZWbfVA at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Gromacs users,
>
>
> I want to classify some peptide aggregates in my simulation box,
> I'd like to know which are the atoms belonging to each 'aggregate' to
> study the aggregate shapes.
>
>
> Is there any gromacs tool suitable for this purpose?
> the best will be to select the atoms according to some kind of
> distance cut-off and then to print an index file containing the list
> of the atomic number for each of the aggregate.
>
>
> Thank you in advance,
> Aishwarya
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 21 Sep 2018 15:02:55 +0200
> From: Aishwarya Dhar <dhar.aishwarya at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Aggregation Analysis
> Message-ID:
>         <CAEod-am_Xzq8y0FeLr67dvWAa6kVALXRWKvJ515xc=
> Yivvt3GQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Gromacs users,
>
>
> I want to classify some peptide aggregates in my simulation box,
> I'd like to know which are the atoms belonging to each 'aggregate' to
> study the aggregate shapes.
>
>
> Is there any gromacs tool suitable for this purpose?
> the best will be to select the atoms according to some kind of
> distance cut-off and then to print an index file containing the list
> of the atomic number for each of the aggregate.
>
>
> Thank you in advance,
> Aishwarya
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 173, Issue 84
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>