[gmx-developers] [Fwd: Re: Water Kinetics]

[David van der Spoel]

-------- Original Message --------
Subject: 	Re: Water Kinetics
Date: 	Sun, 7 Sep 2008 15:23:21 +0300
From: 	Omer Markovitch <omermar at gmail.com>
To: 	David van der Spoel <spoel at xray.bmc.uu.se>
References:
<8c3f24a40809010345k469ae0ccpaf47eec5530ebfc8 at mail.gmail.com>
<48BBCBE6.80403 at xray.bmc.uu.se>



Could you please refer me to the proper resource, about gromacs.
I have tried to post the following question in gromacs-developer list,
but could not post there:
[in short - i am asking where do the energy & coordinates variables are
defined & printed]

========================================
Hello,
I would your help on how to do the following:

I have a 2-body interaction, which I have defined in the file
"topology.top", under the tag "[ pairs ]".
I would like to, during the simulation itself, to generate a new file,
that for each frame will tell me:
(1) Fraction of intact 2-bodies. [ defining intact is not an issue; I
could, for example, use a geometric criterion, or something similar ].
(2) Current total energy, and energy parts.

Now, I am familiar with C language, and not afraid of modifying the
source code.
==>> I will appreciate your help with telling me in what files.c and
which function & variables do the coordinates and energies are stored
and defined <<==
As for the actual printing, I believe that I could simply output my
stuff after the function "write_xtc_traj" is called.

Your help is highly appreciated! Omer Markovitch.
========================================

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Mon, Sep 1, 2008 at 14:03, David van der Spoel <spoel at xray.bmc.uu.se
<mailto:spoel at xray.bmc.uu.se>> wrote:

     Omer Markovitch wrote:

         Dear Sir,
         I would like to tell you about our recent paper, regarding
         hydrogen bond (hbond) kinetics:
         The correlation function of hbonded water pair fits the
         analytical solution of the geminate recombination problem (A+B =
         C, in our case A=B=H2O & C=[H2O]2 ) over several decades in time
         - from sub pico seconds to sub nanoseconds.
         Using only the diffusion constant & contact distance (usualy
         R=3.5 Angstroms) as parameters, the solution gives the
         dissociation & bimolecular recombination rate constants for the
         mentioned reaction.
         For the water pair, we found that, interestingly, recombination
         of a previously bound pair requires first a displacement of a
         3rd molecule, which quickly occupied the vacant binding site
         (hydrogen).
         Activation energies for the forward & backward process are
         similar, rather then being different in the strength of a single
         hbond, also suggesting that a 3rd molecule must first cleave
         before the original pair can recombine.
         The paper is attached here, supporting information is available
         on-line, including an exemplary trajectory movie.
         I'd be happy to discuss this further.
         Best regards, Omer.

     Thanks,

     that is an interesting paper indeed. To what extent do you think
     that the factor of two you find over my previous calculations is
     general? Is this something specific to water? It would be
     interesting to know since I'm writing up a manuscript on a similar
     Luzar/Chandler analysis of other hydrogen bonded systems.

     Cheers,

          *
 
http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000129000008084505000001&idtype=cvips&gifs=yes
 
<http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000129000008084505000001&idtype=cvips&gifs=yes>
 
<http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000129000008084505000001&idtype=cvips&gifs=yes
 
<http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000129000008084505000001&idtype=cvips&gifs=yes>>



         Koby Levy research group,
         Weizmann Institute of Science.
         http://www.weizmann.ac.il/sb/faculty_pages/Levy/



     --
     David van der Spoel, Ph.D., Professor of Biology
     Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala 
University.
     Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
      spoel at gromacs.org <mailto:spoel at gromacs.org>
     http://folding.bmc.uu.se <http://folding.bmc.uu.se/>



-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se