[gmx-users] TIP4P water

[David van der Spoel]

On Thu, 18 Dec 2003, Bing Kim wrote:

>Thanks, guys.
>
>I read the manual. It explain that clearly.
>According to manual, tip4p looks related to "3fd" out of 6 models.
>But can I think tip4p as "3" if I constrain the geometry of tip4p (rigid).
>Sorry for bothering you.
>

forces go to all atoms, as the M site is a linear combination of the 
positions of the other atoms, force will be distribbuted in the same way.
Since a three atom molecule is always planar, the simple linear 
combination is enough.
>Thanks,
>Bing
>
>
>>From: David van der Spoel <spoel at xray.bmc.uu.se>
>>Reply-To: gmx-users at gromacs.org
>>To: gmx-users at gromacs.org
>>Subject: Re: [gmx-users] TIP4P water
>>Date: Thu, 18 Dec 2003 16:29:23 +0100 (CET)
>>
>>On Thu, 18 Dec 2003, Bing Kim wrote:
>>
>> >Hi there.
>> >
>> >I have a question about tip4p water. Gromacs can deal with msite (virtual
>> >site) of tip4p water model which is not real atom.
>> >I am curious how it deal with force on the virtual site.
>> >Should the force be distributed to Oxygen atom or to oxygen and two
>> >hydrogens?
>> >I couldn't find this detailed information from articles.
>>
>>it's described in the manual
>>
>>
>> >Thank you always. Merry Christmas.
>> >Bing
>> >
>> >
>> >>From: David <spoel at xray.bmc.uu.se>
>> >>Reply-To: gmx-users at gromacs.org
>> >>To: gmx-users at gromacs.org
>> >>Subject: Re: [gmx-users] NVE dynamics
>> >>Date: 16 Dec 2003 15:55:34 +0100
>> >>
>> >>On Tue, 2003-12-09 at 23:08, Bing Kim wrote:
>> >> > Hi all.
>> >> >
>> >> > I might have a stupid question.
>> >> > If I run NVE dynamics with single cpu version and parallel version of
>> >> > gromacs, should I see the same result?
>> >>No, because numerical roundoff will lead to different trajectories.
>> >>
>> >>
>> >> > Thanks in advance.
>> >> >
>> >> > Bing Kim
>> >> >
>> >> > _________________________________________________________________
>> >> > Dont worry if your Inbox will max out while you are enjoying the
>> >>holidays.
>> >> > Get MSN Extra Storage!  http://join.msn.com/?PAGE=features/es
>> >> >
>> >> > _______________________________________________
>> >> > gmx-users mailing list
>> >> > gmx-users at gromacs.org
>> >> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> >> > Please don't post (un)subscribe requests to the list. Use the
>> >> > www interface or send it to gmx-users-request at gromacs.org.
>> >>--
>> >>David.
>> >>________________________________________________________________________
>> >>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
>> >>Dept. of Cell and Molecular Biology, Uppsala University.
>> >>Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>> >>phone:	46 18 471 4205		fax: 46 18 511 755
>> >>spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>> >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> >>
>> >>_______________________________________________
>> >>gmx-users mailing list
>> >>gmx-users at gromacs.org
>> >>http://www.gromacs.org/mailman/listinfo/gmx-users
>> >>Please don't post (un)subscribe requests to the list. Use the
>> >>www interface or send it to gmx-users-request at gromacs.org.
>> >
>> >_________________________________________________________________
>> >Have fun customizing MSN Messenger — learn how here!
>> >http://www.msnmessenger-download.com/tracking/reach_customize
>> >
>> >_______________________________________________
>> >gmx-users mailing list
>> >gmx-users at gromacs.org
>> >http://www.gromacs.org/mailman/listinfo/gmx-users
>> >Please don't post (un)subscribe requests to the list. Use the
>> >www interface or send it to gmx-users-request at gromacs.org.
>> >
>>
>>--
>>David.
>>________________________________________________________________________
>>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
>>Dept. of Cell and Molecular Biology, Uppsala University.
>>Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>>phone:	46 18 471 4205		fax: 46 18 511 755
>>spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>_______________________________________________
>>gmx-users mailing list
>>gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-request at gromacs.org.
>
>_________________________________________________________________
>Enjoy the holiday season with great tips from MSN.  
>http://special.msn.com/network/happyholidays.armx
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++