[gmx-users] *.pdb file for the Tip4p/ice model

[Elton Carvalho]

Since ice is a crystal, you can build a crystalline unit cell by hand
(the unit cell will have one or two water molecules, so it's pretty
easy to do it by hand, you just have to be careful to use the same
atom ordering as the topology) and replicate it using gmx genconf so
the crystal has the dimensions you need.

On Thu, Mar 31, 2016 at 1:32 AM, Sheelan Sengupta <s.sengupta at ncl.res.in> wrote:
> will put an ice nuclei (small ice crystal) in a box of water to study the ice nucleation. water and ice will be modeled by tip4p.
>
> Sheelan S C
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Christopher Neale [chris.neale at alum.utoronto.ca]
> Sent: Wednesday, March 30, 2016 11:25 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] *.pdb file for the Tip4p/ice model
>
> Need it for what? To solvate a solute with genbox or for some other sytem setup needs? Common protocol would be to simply use tip4p.gro and then to equilibrate it with the new tip4p/ice parameters. tip4p.gro is in share/gromacs/top/
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sheelan Sengupta <s.sengupta at ncl.res.in>
> Sent: 30 March 2016 05:45
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] *.pdb file for the Tip4p/ice model
>
> need the *.pdb file of Tip4p/ice model. Please help.
>
> Regards,
> Sheelan S C
> Phys Chem Div
>
> ________________________________
>
> Disclaimer:
>
> This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx
> --
> 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
>
> * 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.
>
> ________________________________
>
> Disclaimer:
>
> This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/files/TermsAndConditions/WebmailDisclamer.aspx
> --
> 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.



-- 
Elton Carvalho