[gmx-users] gromacs.org_gmx-users Digest, Vol 173, Issue 86
Aishwarya Dhar
dhar.aishwarya at gmail.com
Sat Sep 22 16:18:36 CEST 2018
RE: Aggregatiion Analysis
with gmx make_ndx we can make index of the atom we already know, but our
problem is to identify which are the atom of interest.
Aishwarya
On Sat, Sep 22, 2018 at 8:13 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: Aggregation Analysis (Soham Sarkar)
> 2. Re: gromacs.org_gmx-users Digest, Vol 173, Issue 84
> (Aishwarya Dhar)
> 3. caculate free energy (T?ng Ho?ng)
> 4. Re: Lateral pressure (Alex)
> 5. problem (AKANXA TIWARI)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 Sep 2018 21:13:11 +0530
> From: Soham Sarkar <soham9038 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Aggregation Analysis
> Message-ID:
> <CA+fBeddZT87zPk=qF=fg2TTQF4A2HHsyFKDpAmgDOY6UVQJU8w at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> gmx make_ndx is the tool to use for making grouos of your choice
>
> On Fri, 21 Sep 2018, 8:51 pm Aishwarya Dhar, <dhar.aishwarya at gmail.com>
> wrote:
>
> > 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
> > --
> > 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: 2
> Date: Fri, 21 Sep 2018 16:50:17 +0200
> From: Aishwarya Dhar <dhar.aishwarya at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 173, Issue
> 84
> Message-ID:
> <CAEod-anN1dSwwz0W_t=paipi-uYE4Oj7kcCBNNFRGvF=SGgv7Q@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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:
>
> > Send gromacs.org_gmx-users mailing list submissions to
> > gromacs.org_gmx-users at 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-request at maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> > gromacs.org_gmx-users-owner at 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: 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*
> > --
> > 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.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r
> > det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r
> > det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/
> >
> > E-mailing Uppsala University means that we will process your personal
> > data. For more information on how this is performed, please read here:
> > http://www.uu.se/om-uu/dataskydd-personuppgifter/
> >
> > ------------------------------
> >
> > 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
> >
> >
> > ------------------------------
> >
> > --
> > 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.
> >
> > End of gromacs.org_gmx-users Digest, Vol 173, Issue 84
> > ******************************************************
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 21 Sep 2018 09:48:22 +0700
> From: T?ng Ho?ng <hoangtung9597 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] caculate free energy
> Message-ID:
> <CAFn5YueFZGyu-szEvriY4bdAXMmvGC2V=jeOZ8XC0Sq
> -zXLwLw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi, it me again. I'm trying to calculate free energy for protein ligand. I
> restrain protein ligand and dG =102kj for protein. but i know the value
> must be =64 kj i read that in paper( tutorlal). i think the different is dG
> restrain but why is so error? and how can i calculate for true? i don't
> know how to calculate this dG restrain or negative it.
> Tks for your repply.
> --
> Ho?ng T?ng / student
> hoangtung9597 at gmail.com / +(84) 0928 478 789
>
> University of Medicine and Pharmacy I Ho Chi Minh City
> 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> <https://htmlsig.com/signatures/0001DP594H>
>
> [image: Facebook] <https://htmlsig.com/t/000001DK2V24> [image: Skype]
> <https://htmlsig.com/t/000001DH4S28>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 21 Sep 2018 03:12:05 -0600
> From: Alex <nedomacho at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Lateral pressure
> Message-ID: <befb658d-9701-b5c3-041a-8849665ae2cf at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> gmx energy lets you plot the components of the pressure tensor, the Z-Z
> term is one of them.
>
> Alex
>
>
> On 9/21/2018 2:52 AM, Candy Deck wrote:
> > Dear Gromacs Users,
> >
> > Is there a way to get the lateral pressure with Gromacs ?
> > I am willing to get the variation of pressure along z.
> >
> > Thanks !
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 22 Sep 2018 11:36:02 +0530
> From: AKANXA TIWARI <akanxatiwari24 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] problem
> Message-ID:
> <CAAbXdB3usgdwFOEjddYGMd0g9+_PxCC3Yp67PJC8EU3YpFBCag at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> hello
> i am simulating tubulin heterodimer . after giving command for solvent
> adding i got a warning on screen what should i do.
>
> Initialising inter-atomic distances...
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
> based on residue and atom names, since they could not be
> definitively assigned from the information in your input
> files. These guessed numbers might deviate from the mass
> and radius of the atom type. Please check the output
> files if necessary.
>
> NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
> from the source below. This means the results may be different
> compared to previous GROMACS versions.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> A. Bondi
> van der Waals Volumes and Radii
> J. Phys. Chem. 68 (1964) pp. 441-451
> -------- -------- --- Thank You --- -------- --------
>
> Generating solvent configuration
> Will generate new solvent configuration of 7x7x7 boxes
> Solvent box contains 202791 atoms in 67597 residues
> Removed 17799 solvent atoms due to solvent-solvent overlap
> Removed 10800 solvent atoms due to solute-solvent overlap
> Sorting configuration
> Found 1 molecule type:
> SOL ( 3 atoms): 58064 residues
> Generated solvent containing 174192 atoms in 58064 residues
> Writing generated configuration to 1jff_solv.gro
>
> Output configuration contains 182636 atoms in 58902 residues
> Volume : 1882.42 (nm^3)
> Density : 1006.94 (g/l)
> Number of solvent molecules: 58064
>
> Processing topology
> Adding line for 58064 solvent molecules with resname (SOL) to topology file
> (topol.top)
>
> Back Off! I just backed up topol.top to ./#topol.top.1#
>
> GROMACS reminds you: "She's Not Bad, She's Just Genetically Mean" (Captain
> Beefheart)
>
>
> ------------------------------
>
> --
> 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.
>
> End of gromacs.org_gmx-users Digest, Vol 173, Issue 86
> ******************************************************
>
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