Thanks alot Goga N and Raman Preet Singh, I have to simulate the polymer thin film of the order of sub nanometer length scale, though I have gone through the DPDMacs, am able to run simple DPD calculations, but haven't found any reference article that used DPD-MACS. In addition to that we cannot simply calculate any thermodynamic properties like Delta_G and Delta_H, using DPDMACS. As Gromcs Approach of free-enrgy calculation we cannot simply implement to It. I hope this would topic of future interest those who want to develop. However most of the references i have found either uses LAMMPS, DL_Meso and Mesodyn. But post procssing needs to be coded on their own,I hope we should go ahead with well tested LAMMPS.
Best Praveen On Tue, Oct 24, 2017 at 7:01 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. Contact map (sp...@iacs.res.in) > 2. Re: DPD in Groamcs (Raman Preet Singh) > 3. Re: DPD in Groamcs (Raman Preet Singh) > 4. Re: DPD in Groamcs (Goga, N.) > 5. (no subject) (limingru) > 6. Re: Drude polarizable simulations (Justin Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 24 Oct 2017 17:28:38 +0530 > From: sp...@iacs.res.in > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Contact map > Message-ID: > <20171024172838.horde.dkozh3iro8jn-6chod0w...@mailweb.iacs.res.in> > Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes > > Hi all > I want to generate a contact map for all the residues of lysozyme protein. > I am using gmx mdmat to generate this. Can I generate a text file (which > can be open in Grace) except the image files(eg: xpm file)? Please let me > know the particular flag which I can use to get a *.xvg file. > > Thanks > Sunipa Sarkar > > > ------------------------------ > > Message: 2 > Date: Tue, 24 Oct 2017 12:27:09 +0000 > From: Raman Preet Singh <ramanpreetsi...@hotmail.com> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] DPD in Groamcs > Message-ID: > <MA1PR01MB02647E33FAB041CD06BBDE45B3470@MA1PR01MB0264. > INDPRD01.PROD.OUTLOOK.COM> > > Content-Type: text/plain; charset="utf-8" > > I was looking for DPD in Gromacs too but in vain. You may try DPDmacs, > POLY DL or LAMPPS. > > ------------------------------ > > Message: 3 > Date: Tue, 24 Oct 2017 12:32:19 +0000 > From: Raman Preet Singh <ramanpreetsi...@hotmail.com> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] DPD in Groamcs > Message-ID: > <MA1PR01MB0264F0C6F85A00769FD6F566B3470@MA1PR01MB0264. > INDPRD01.PROD.OUTLOOK.COM> > > Content-Type: text/plain; charset="utf-8" > > Forgot to mention Materials Studio..... An extremely easy-to-use software > but comes at a hefty license fee. > > On Oct 24, 2017 5:57 PM, Raman Preet Singh <ramanpreetsi...@hotmail.com< > mailto:ramanpreetsi...@hotmail.com>> wrote: > > I was looking for DPD in Gromacs too but in vain. You may try DPDmacs, > POLY DL or LAMPPS. > > ------------------------------ > > Message: 4 > Date: Tue, 24 Oct 2017 15:30:34 +0300 > From: "Goga, N." <n.g...@rug.nl> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] DPD in Groamcs > Message-ID: > <CAAHQ6H4=7g0d1ucJY_qAUg62v_tUYT3OtYqP+HZQdtMreEWikg@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Friend, > > I may have some older version of DPD-gromacs. However, I am not sure for > what you need it. Being trial, that version might not be completely free of > errors. > > Nicu > > On Tue, Oct 24, 2017 at 3:27 PM, Raman Preet Singh < > ramanpreetsi...@hotmail.com> wrote: > > > I was looking for DPD in Gromacs too but in vain. You may try DPDmacs, > > POLY DL or LAMPPS. > > -- > > 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. > > > > > ------------------------------ > > Message: 5 > Date: Tue, 24 Oct 2017 21:24:28 +0800 > From: "limingru" <mr...@sina.com> > To: "gmx-users" <gmx-us...@gromacs.org> > Subject: [gmx-users] (no subject) > Message-ID: <20171024132428.dfb338100...@webmail.sinamail.sina.com.cn> > Content-Type: text/plain; charset=GBK > > Dear all, I want to use GMX to simulate ethanol solution > interaction with macromolecular in a polarizable force filed. Whether the > macromolecular and ethanol PDB files need adding Drude particles? and how > to produce an ethanol.itp file for Drude2013 force field? Do the Drude2013 > force field can be ran in the GMX v4.6.5? Thanks in advance. > Best wishes! > -------------------------------- > > > School of Nuclear Sci and Tec, > Beijing Normal University > > Room.110,Teaching-Research Complex, > NO.10 WenHuiYuan St,Haiding District, > Beijing 100089,China > > > > > > > ------------------------------ > > Message: 6 > Date: Tue, 24 Oct 2017 09:31:36 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Drude polarizable simulations > Message-ID: <e6050f19-1d1f-d3a3-2a89-0b0acfbcd...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 10/24/17 12:08 AM, limingru wrote: > > Hello Justin, Many thanks for your answer. Another > question is that whether I need adding some Drude particles in my PDB file > of DNA or Protein in the simulation process, if any, how to modify the PDB > file? I > > pdb2gmx will build everything for you. > > > have been using the gmx v4.6.5 to do something. I don't know if this > version can run Drude polarizable simulations. > > No, you need to check out the developmental version of the code and use > the Drude branch. > > -Justin > > > I am going to do protein interaction with organic solution (e.g. ethanol > or methanol, etc) in Drude2013 force filed using gromacs software. Would > you please give me some warnings? I think it will give me more clear > direction and bring me convenience in simulation process. Thanks a lot. > > Best wishes! > > -------------------------------- > > > > > > School of Nuclear Sci and Tec, > > Beijing Normal University > > > > Room.110,Teaching-Research Complex, > > NO.10 WenHuiYuan St,Haiding District, > > Beijing 100089,China > > > > > > > > > > > > > > ----- Original Message ----- > > From: gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: gromacs.org_gmx-users Digest, Vol 162, Issue 88 > > Date: 2017-10-24 01:10 > > > > > > 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: DPD in Groamcs (Goga, N.) > > 2. Re: Conversion Amber to Gromacs (Thomas Piggot) > > 3. Re: Conversion Amber to Gromacs (Mark Abraham) > > 4. Drude polarizable simulations (limingru) > > 5. Re: Drude polarizable simulations (Justin Lemkul) > > 6. Doubt about thermostat in MD (Varvdekar Bhagyesh Rajendra) > > ---------------------------------------------------------------------- > > Message: 1 > > Date: Mon, 23 Oct 2017 13:54:20 +0300 > > From: "Goga, N." <n.g...@rug.nl> > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] DPD in Groamcs > > Message-ID: > > <CAAHQ6H62djzjnd=pJzUSCzz9GVFu9Gxtk32yCotdjgCPCisErA@mail. > gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > Dear Kumar, > > Why do you need DPD? > > Nicu > > On Sun, Oct 22, 2017 at 11:28 PM, Dallas Warren < > dallas.war...@monash.edu> > > wrote: > >> Not directly, though one of developers might have better insight into > >> that. Though there are requests / proposals to add it > >> https://redmine.gromacs.org/issues/1885 > >> > >> There is DPDmacs http://www.apmaths.uwo.ca/~mkarttu/dpdmacs.shtml > >> Catch ya, > >> > >> Dr. Dallas Warren > >> Drug Delivery, Disposition and Dynamics > >> Monash Institute of Pharmaceutical Sciences, Monash University > >> 381 Royal Parade, Parkville VIC 3052 > >> dallas.war...@monash.edu > >> --------------------------------- > >> When the only tool you own is a hammer, every problem begins to > resemble a > >> nail. > >> > >> > >> On 21 October 2017 at 23:53, praveen kumar <praveen...@gmail.com> > wrote: > >>> Dear all > >>> is there any possibility of performing dissipative particle dynamics > >> (DPD) > >>> in gromacs? > >>> > >>> Thanks in Advance > >>> Praveen > >>> -- > >>> 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. > >> -- > >> 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. > >> > > ------------------------------ > > Message: 2 > > Date: Mon, 23 Oct 2017 12:13:14 +0100 > > From: Thomas Piggot <t.pig...@soton.ac.uk> > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Conversion Amber to Gromacs > > Message-ID: <afca89bc-2553-90d1-b2ab-009a4e819...@soton.ac.uk> > > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi, > > The multiplicity/periodicity is the same but always positive in GROMACS. > > Kd in GROMACS is the AMBER value multiplied by 4.184 then divided by > > IDIVF (the entry after names in AMBER file). The phase is the same. > > For more info on why see ambermd.org/formats.html#parm.dat > > Cheers > > Tom > > On 23/10/17 10:09, Elisa Pieri wrote: > >> Hello again, > >> > >> sorry I wasn't very clear perhaps..we are trying to modify directly the > >> ffbonded.itp file (together with all the other interested ones) in the > >> Amber94 force field in order to include the Amber Lipids17 force field. > We > >> added most of the parameters with no problems (bond equilibrium lengths, > >> constants, bending and so on), but we were not able to understand what > is > >> the conversion factor for torsion parameters between the Amber software > >> Suite and Gromacs. I know that in the Amber package, the dihedral force > >> constant is expressed in Kcal/mol, but I couldn't understand what are > the > >> units (and therefore how to convert the parameters) in Gromacs. > >> > >> Any idea? > >> Elisa > >> > >> On Fri, Oct 20, 2017 at 7:17 PM, p.kartheek <kartheekpi...@gmail.com> > wrote: > >> > >>> ParmEd (https://parmed.github.io/ParmEd/html/parmed.html) would be the > >>> appropriate software for converting topologies. > >>> This is the parm.py script I have employed, supply amber topologies > >>> file.prmtop and file.inpcrd as input and amber.save option will give > >>> converted gromacs topologies as output. > >>> > >>> import parmed as pmd > >>> #amber = pmd.load_file('prmtop', 'inpcrd') > >>> amber = pmd.load_file('new24_ang.prmtop', 'new24_ang.inpcrd') > >>> #save a GROMACS topology and GRO file > >>> amber.save('new24_ang.top') > >>> amber.save('new24_ang.gro') > >>> > >>> > >>> ---------------------------------------------- > >>> P. Kartheek, > >>> PhD Candidate, Computational Biophysical Chemistry, > >>> Center for Computational Natural Sciences and Bioinformatics, > >>> International Institute of Information Technology, > >>> Marimuthu Krishan Group, > >>> 9701577399, > >>> karthee...@research.iiit.ac.in, > >>> > >>> > >>> On Fri, Oct 20, 2017 at 10:30 PM, p.kartheek <kartheekpi...@gmail.com> > >>> wrote: > >>> > >>>> You can do with ParmEd > >>>> On Oct 20, 2017 10:07 PM, "Elisa Pieri" <elisa.pi...@univ-amu.fr> > wrote: > >>>> > >>>>> Hello GMX users/developers, > >>>>> > >>>>> we are trying to add the Amber lipids17 forcefield to the Amber99 > >>>>> forcefield implemented in Gromacs. We are a little bit lost on the > >>> torsion > >>>>> parameters: how to convert the constant from Amber to Gromacs? > >>>>> > >>>>> Thank you in advance! > >>>>> Elisa > >>>>> -- > >>>>> 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. > >>>>> > >>> -- > >>> 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. > >>> > > -- > ================================================== > > 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.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > > > ------------------------------ > > -- > 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 162, Issue 91 > ****************************************************** > -- Thanks & Regards Dr.Praveen Kumar Sappidi, National Post Doctoral Fellow. Computational Nanoscience Laboratory, Chemical Engineering Department, IIT Kanpur,India-208016 -- 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.
