Dear Chris, Yes, tip4p.gro worked well.
Thank you On Wed, Jul 5, 2017 at 10:55 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. TIP4P/ice pdb file (G R) > 2. Re: simulation at different temperature (Alex) > 3. Re: simulation at different temperature (Alex) > 4. Re: TIP4P/ice pdb file (Christopher Neale) > 5. Re: TIP4P/ice pdb file (Christopher Neale) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Jul 2017 21:57:26 +0300 > From: G R <golnaz.c...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] TIP4P/ice pdb file > Message-ID: > <CAGFO7SHoX6-KJO8T8DkfM2rdW=1nUdWcvy80vm7i92KOj1nA-g@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear All, > > I would like to simulate water using TIP4P/ice potential. My question is > that how can I generate .gro file for this simulation? > I will use TIP4P/ice topology that is available in SklogWiki, but I cannot > understand how can I generate .gro file for this topology. Can I easily use > TIP4P.gro that is available in share/top? If yes, how can I modify > TIP4P.gro file to use with TIP4P/ice potential? > > Best regards, > Golnaz > > > ------------------------------ > > Message: 2 > Date: Wed, 5 Jul 2017 13:09:00 -0600 > From: Alex <nedoma...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Cc: Discussion list for GROMACS users > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] simulation at different temperature > Message-ID: > <CAMJZ6qGBvS2e9HpVjMEPGvXG5yWAXeFj0QOSOC_riD4+HR4rJg@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > I don't understand the objection. This _is_ full dynamics of the system > containing behavior at all desired temperatures. > After it's done, you can easily split trajectories into the desired > annealing regions. Alternatively, you could simply script this as a > sequence of separate runs based on mdp's with gradually increasing T, > simply throw away a few first ns of each simulation before analyzing. > > Alex > > On Wed, Jul 5, 2017 at 12:51 PM, Alex Mathew <alexmathe...@gmail.com> > wrote: > > > Dear Alex, > > > > I guess this is annealing and which will give only one output.xtc, I'm > > looking for full dynamics of the system (say 100 ns for each temperature, > > 300 K,305 K....340 K ). Further, I need to compare the results with each > > other. > > > > Thank you. > > -- > > 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: 3 > Date: Wed, 5 Jul 2017 13:09:00 -0600 > From: Alex <nedoma...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Cc: Discussion list for GROMACS users > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] simulation at different temperature > Message-ID: > <CAMJZ6qGBvS2e9HpVjMEPGvXG5yWAXeFj0QOSOC_riD4+HR4rJg@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > I don't understand the objection. This _is_ full dynamics of the system > containing behavior at all desired temperatures. > After it's done, you can easily split trajectories into the desired > annealing regions. Alternatively, you could simply script this as a > sequence of separate runs based on mdp's with gradually increasing T, > simply throw away a few first ns of each simulation before analyzing. > > Alex > > On Wed, Jul 5, 2017 at 12:51 PM, Alex Mathew <alexmathe...@gmail.com> > wrote: > > > Dear Alex, > > > > I guess this is annealing and which will give only one output.xtc, I'm > > looking for full dynamics of the system (say 100 ns for each temperature, > > 300 K,305 K....340 K ). Further, I need to compare the results with each > > other. > > > > Thank you. > > -- > > 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: 4 > Date: Wed, 5 Jul 2017 19:54:53 +0000 > From: Christopher Neale <chris.ne...@alum.utoronto.ca> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se>, " > gmx-us...@gromacs.org" > <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] TIP4P/ice pdb file > Message-ID: > <YTOPR01MB039370AACEFA5F4C7E407A8DC5D40@YTOPR01MB0393. > CANPRD01.PROD.OUTLOOK.COM> > > Content-Type: text/plain; charset="us-ascii" > > I believe that you can use any 4-point water model .gro for any 4-point > water topology (or likewise for 3-point water models). Did you try it yet? > If so, what problem are you running into specifically? > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of G R < > golnaz.c...@gmail.com> > Sent: 05 July 2017 14:57:26 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] TIP4P/ice pdb file > > Dear All, > > I would like to simulate water using TIP4P/ice potential. My question is > that how can I generate .gro file for this simulation? > I will use TIP4P/ice topology that is available in SklogWiki, but I cannot > understand how can I generate .gro file for this topology. Can I easily use > TIP4P.gro that is available in share/top? If yes, how can I modify > TIP4P.gro file to use with TIP4P/ice potential? > > Best regards, > Golnaz > -- > 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: Wed, 5 Jul 2017 19:54:53 +0000 > From: Christopher Neale <chris.ne...@alum.utoronto.ca> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se>, " > gmx-us...@gromacs.org" > <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] TIP4P/ice pdb file > Message-ID: > <YTOPR01MB039370AACEFA5F4C7E407A8DC5D40@YTOPR01MB0393. > CANPRD01.PROD.OUTLOOK.COM> > > Content-Type: text/plain; charset="us-ascii" > > I believe that you can use any 4-point water model .gro for any 4-point > water topology (or likewise for 3-point water models). Did you try it yet? > If so, what problem are you running into specifically? > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of G R < > golnaz.c...@gmail.com> > Sent: 05 July 2017 14:57:26 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] TIP4P/ice pdb file > > Dear All, > > I would like to simulate water using TIP4P/ice potential. My question is > that how can I generate .gro file for this simulation? > I will use TIP4P/ice topology that is available in SklogWiki, but I cannot > understand how can I generate .gro file for this topology. Can I easily use > TIP4P.gro that is available in share/top? If yes, how can I modify > TIP4P.gro file to use with TIP4P/ice potential? > > Best regards, > Golnaz > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 159, Issue 25 > ****************************************************** > -- 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.