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-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. 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.mu...@ut.ee> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] GROMACS user workshop > Message-ID: <c9d9718b-5539-0590-41c8-ebb9a2f6a...@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.mu...@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.markl...@kemi.uu.se> > To: "<gmx-us...@gromacs.org> GROMACS users" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] protein dna pulling > Message-ID: <ea2050c5-53d6-4099-8eb3-d3a7d5819...@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.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > On 27 Aug 2018, at 20:11, abhisek Mondal <abhisek.m...@gmail.com<mailto: > abhisek.m...@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-requ...@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....@helmholtz-muenchen.de> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Nonbonded energy of 1-4 interactions > Message-ID: > <dddbfff1-8697-4f3c-8db3-5cf422486...@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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Nonbonded energy of 1-4 interactions > Message-ID: <c7fc0460-812f-ec67-8f9b-277ce31b1...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 5 > Date: Fri, 21 Sep 2018 15:00:56 +0200 > From: Aishwarya Dhar <dhar.aishwa...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Aggregation Analysis > Message-ID: > <CAEod-am+FJTDCXp_LbMoqd2A4szH_WP5HGcnbrR2CoszZWbfVA@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.aishwa...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] Aggregation Analysis > Message-ID: > <CAEod-am_Xzq8y0FeLr67dvWAa6kVALXRWKvJ515xc= > yivvt...@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-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 173, Issue 84 > ****************************************************** > -- 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.
