Hi, Thanks Alex. I have now solved the problem. I assumed ³gen - pairs = yes² within [ Defaults ] of the topology was generating automatically a list of pairs of 1-4 interactions as well as modifying the LJ and QQ parameters for those interactions. I have now listed the 1-4 pairs within [ Pairs ] and it has led to the correct equilibrium bond length. Cheers, Amanda
On 28/06/2017, 19:22, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of 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: Atom types comparison between CGenFF and Charm36FF > (Justin Lemkul) > 2. Re: Atom types comparison between CGenFF and Charm36FF > (Mohsen Ramezanpour) > 3. Re: Using SLLOD to find Viscosity (nishi kashyap) > 4. Deform a liquid (nishi kashyap) > 5. Anybody using Silica InterfaceFF on Gromacs? > (Diez Fernandez, Amanda) > 6. Re: Anybody using Silica InterfaceFF on Gromacs? (Alex) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 28 Jun 2017 10:21:32 -0600 >From: Justin Lemkul <jalem...@vt.edu> >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Atom types comparison between CGenFF and > Charm36FF >Message-ID: <350dd743-bdfa-76ee-a401-039cadaf1...@vt.edu> >Content-Type: text/plain; charset=utf-8; format=flowed > > > >On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote: >> Thanks Justin for your comment. >> >> I have a bit of difficulty for the finding the analog parts to these two >> parts. >> >> Is there any database (preferably with shapes) for the molecules >>available >> in charmmFF? >> > >The CHARMM topology files have full residue names and chemical structure >drawings. Within the toppar directory (download the tarball from our >site), >just grep -r "RESI" * > >If you have additional questions about this or CHARMM parametrization, >contact >me off list as this is not really a GROMACS issue. > >-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 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >================================================== > > >------------------------------ > >Message: 2 >Date: Wed, 28 Jun 2017 10:38:13 -0600 >From: Mohsen Ramezanpour <ramezanpour.moh...@gmail.com> >To: Discussion list for GROMACS users <gmx-us...@gromacs.org> >Subject: Re: [gmx-users] Atom types comparison between CGenFF and > Charm36FF >Message-ID: > <CAERzrhskVqO0FhgWg0JiE2AyY-M9C6aGPNnM=ymeezep5hz...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Thanks, Justin. > >Sure. > >On Wed, Jun 28, 2017 at 10:21 AM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote: >> >>> Thanks Justin for your comment. >>> >>> I have a bit of difficulty for the finding the analog parts to these >>>two >>> parts. >>> >>> Is there any database (preferably with shapes) for the molecules >>>available >>> in charmmFF? >>> >>> >> The CHARMM topology files have full residue names and chemical structure >> drawings. Within the toppar directory (download the tarball from our >> site), just grep -r "RESI" * >> >> If you have additional questions about this or CHARMM parametrization, >> contact me off list as this is not really a GROMACS issue. >> >> >> -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 >> >> jalem...@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-requ...@gromacs.org. >> > > > >-- >*Rewards work better than punishment ...* > > >------------------------------ > >Message: 3 >Date: Wed, 28 Jun 2017 12:56:47 -0400 >From: nishi kashyap <nishikashya...@gmail.com> >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Using SLLOD to find Viscosity >Message-ID: > <cafyo1favztsnfgt1i5ry2eqhrk_mxymsuyjwua-9jopr__w...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >I have read both things thoroughly. I am new to this and so having a hard >time gathering basic concepts. >So, correct me if I am wrong: > >To calculate shear viscosity in a PEG system: >1. Created a stable system and given cos_acceleration =0.05 >2. Since I would know A(amplitude of acceleration),rho and k(wave index >number), I can find out the viscosity > >Still, how do I find shear rate from that? Ideally, I should be changing >shear rate and finding viscosity. How can I do that ? > >I might be asking very basic things but please help me here. > > >On Sat, Jun 3, 2017 at 3:25 AM, David van der Spoel <sp...@xray.bmc.uu.se> >wrote: > >> On 02/06/17 22:12, nishi kashyap wrote: >> >>> Thanks for replying. >>> I have also tried that before. If we give the whole system the same >>> acceleration, then it wouldn't experience any shear. That was what I >>>was >>> observing also. >>> Is there no way/ inbuilt method which use SLLOD , like in LAMMPS ? >>> >> >> Please read my email again carefully, and those references, in >>particular >> the Hess paper. >> >> >> >>> On Fri, Jun 2, 2017 at 4:09 PM, David van der Spoel >>><sp...@xray.bmc.uu.se >>> > >>> wrote: >>> >>> On 02/06/17 22:02, nishi kashyap wrote: >>>> >>>> Hi >>>>> I have a system of PEG for which I want to find viscosity. I want to >>>>>use >>>>> SLLOD equations to find viscosity for a specific shear rate. I have >>>>>read >>>>> allot about different ways , even tried to use 'deform'. But I did >>>>>not >>>>> understand what do you mean by "off diagonal elements in a single >>>>> array". >>>>> I >>>>> am not able to understand. And also how do you intend to find shear >>>>>rate >>>>> proceeding from that. >>>>> Could you please give some insight. >>>>> I would prefer if you just tell me how to use SLLOD equations? I >>>>>really >>>>> need it, I have been trying this for so long. >>>>> Thank You >>>>> >>>>> Try using the cos_accel with a few different values. >>>>> >>>> See J. Chem. Phys. 119 pp. 7308-7317 (2003) and J. Chem. Phys. 116, >>>>209 >>>> 2002 >>>> >>>> -- >>>> David van der Spoel, Ph.D., Professor of Biology >>>> Head of Department, Cell & Molecular Biology, Uppsala University. >>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >>>> http://www.icm.uu.se >>>> -- >>>> 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. >>>> >>>> >>> >>> >>> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> 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. >> > > > >-- >Nishi Kashyap >Undergraduate >Chemical Engineering >IIT Delhi > > >------------------------------ > >Message: 4 >Date: Wed, 28 Jun 2017 13:06:10 -0400 >From: nishi kashyap <nishikashya...@gmail.com> >To: gmx-us...@gromacs.org >Subject: [gmx-users] Deform a liquid >Message-ID: > <CAFYO1fb0HaZXNPgVPLD9GJrJ88+Pfpt8n5MUiFyC==n1uee...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi >I am new to gromacs and so a basic doubt. >How do we use 'deform' as specified in non equilibrium section of mdp >file? >Considering I have a box of polymer to be given some shear only in x >direction, what should be the arguments? > > >-- >Nishi Kashyap >Undergraduate >Chemical Engineering >IIT Delhi > > >------------------------------ > >Message: 5 >Date: Wed, 28 Jun 2017 17:49:04 +0000 >From: "Diez Fernandez, Amanda" <amanda.die...@imperial.ac.uk> >To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> >Subject: [gmx-users] Anybody using Silica InterfaceFF on Gromacs? >Message-ID: <d579aa9d.f44e%amanda.die...@imperial.ac.uk> >Content-Type: text/plain; charset="us-ascii" > >Hi, >I converted the InterfaceFF silica parameters to use in Gromacs (and to >be compatible with the AMBER forcefield) and have gotten some problems, >namely I am getting a slightly bigger equilibrium bond length than I >should. >I was wondering if there were other Gromacs users out there that have >used InterfaceFF silica parameters in Gromacs. > >Many thanks, >Amanda > > >------------------------------ > >Message: 6 >Date: Wed, 28 Jun 2017 12:22:46 -0600 >From: Alex <nedoma...@gmail.com> >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs? >Message-ID: <925932e6-1a3f-b11a-72fb-b2b1f6c63...@gmail.com> >Content-Type: text/plain; charset=utf-8; format=flowed > >This community is mostly focused on other things. If you have solid >silica under a non-native (to Gromacs) forcefield and all the bonded >parameters have been copied correctly, there may be issues with your >partial charges, LJ parameters, and mixing rules. Also make sure your >original forcefield uses the same approach to neighbor searching as >Gromacs does. Also to my knowledge, very few solid-state potentials use >the childish 1-4 pair interaction. > >Alex > >On 6/28/2017 11:49 AM, Diez Fernandez, Amanda wrote: >> Hi, >> I converted the InterfaceFF silica parameters to use in Gromacs (and to >>be compatible with the AMBER forcefield) and have gotten some problems, >>namely I am getting a slightly bigger equilibrium bond length than I >>should. >> I was wondering if there were other Gromacs users out there that have >>used InterfaceFF silica parameters in Gromacs. >> >> Many thanks, >> Amanda > > > >------------------------------ > >-- >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 158, Issue 181 >******************************************************* -- 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.