[gmx-users] TIP4P/ice pdb file

G R golnaz.chem at gmail.com
Thu Jul 6 09:42:40 CEST 2017


Dear Chris,

Yes, tip4p.gro worked well.

Thank you

On Wed, Jul 5, 2017 at 10:55 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> 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.chem at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] TIP4P/ice pdb file
> Message-ID:
>         <CAGFO7SHoX6-KJO8T8DkfM2rdW=1nUdWcvy80vm7i92KOj1nA-g at 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 <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] simulation at different temperature
> Message-ID:
>         <CAMJZ6qGBvS2e9HpVjMEPGvXG5yWAXeFj0QOSOC_riD4+HR4rJg at 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 <alexmathewmd at 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/
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> >
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 5 Jul 2017 13:09:00 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] simulation at different temperature
> Message-ID:
>         <CAMJZ6qGBvS2e9HpVjMEPGvXG5yWAXeFj0QOSOC_riD4+HR4rJg at 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 <alexmathewmd at 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-request at gromacs.org.
> >
>
>
> ------------------------------

Message: 4
> Date: Wed, 5 Jul 2017 19:54:53 +0000
> From: Christopher Neale <chris.neale at alum.utoronto.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>, "
> gmx-users at gromacs.org"
>         <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] TIP4P/ice pdb file
> Message-ID:
>         <YTOPR01MB039370AACEFA5F4C7E407A8DC5D40 at 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-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of G R <
> golnaz.chem at gmail.com>
> Sent: 05 July 2017 14:57:26
> To: gromacs.org_gmx-users at 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-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 5 Jul 2017 19:54:53 +0000
> From: Christopher Neale <chris.neale at alum.utoronto.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>, "
> gmx-users at gromacs.org"
>         <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] TIP4P/ice pdb file
> Message-ID:
>         <YTOPR01MB039370AACEFA5F4C7E407A8DC5D40 at 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-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of G R <
> golnaz.chem at gmail.com>
> Sent: 05 July 2017 14:57:26
> To: gromacs.org_gmx-users at 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-request at 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
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