[gmx-users] Topology file for D2O
dmobley at gmail.com
Tue Mar 27 16:33:09 CEST 2007
I am not an expert about heavy water -- but it does seem strange to me
to think that you could get "heavy water" just by changing the mass of
the hydrogens in a conventional water model. The *only* thing this
will affect is the kinetic energy and mass of water. Presumably
changing hydrogen to deuterium *should* also affect other things, such
as perhaps slightly altering the electrostatics or dispersion
interactions, or the water molecule shape. I'm no expert -- but I bet
there's more to it than just a slight change in mass.
Maybe you might already know part of the answer to this: Why is it you
want to run with D2O instead of regular water? I'm guessing it's
because you expect some difference in behavior... Should that really
be due exclusively to a difference in mass?
On 3/27/07, Andrés N. McCarthy <amccarthy at iflysib.unlp.edu.ar> wrote:
> Hi Joys Yu,
> In addition to Tserks comments you might want to use a more specifically
> developed heavy water model.
> Here is a reference you may find usefull:
> An effective pair potential for heavy water - J. Raul Grigera
> The Journal of Chemical Physics -- May 8, 2001 -- Volume 114, Issue 18, pp.
> I have created a topology file based on these parameters for a cooperation I
> did some time back. If you are interested I can email the topology & modified
> FF fiels to you.
> El Martes, 27 de Marzo de 2007 03:29, Joys Yu escribió:
> > Dear all,
> > I would like to do simulation of bulk heavy water
> > (D2O). So first thing, I need to get the topology file
> > of D2O. In fact, I would like to use SPC H2O. I just
> > need to change the mass of H in H2O from 1.008 to
> > 2.016.
> > I would like to use gromacs force field(#7). So I
> > revised ffgms.atp. I changed the mass of water
> > hydrogen from 1.008 to 2.016.
> > When I use pdbtogmx to get the topology, it seems
> > fine. I have a bulk heavy water, which has 674 D2O.
> > Here is some of the running results from pdbtogmx:
> > Now there are 674 residues with 2022 atoms
> > Making bonds...
> > Opening library file
> > /home/gromacs-d/share/top/aminoacids.dat
> > Number of bonds was 1348, now 1348
> > Generating angles, dihedrals and pairs...
> > There are 0 dihedrals, 0 impropers, 674 angles
> > 0 pairs, 1348 bonds and 0 virtual
> > sites
> > Total mass 13501.164 a.m.u.
> > Total charge 0.000 e
> > The total mass for 674 D2O is correct: 674 * 20.03 =
> > 13501.164
> > Here is the topology file that I got for D2O:
> > ;
> > ; File 'd2o.top' was generated
> > ; By user: Joys (1002)
> > ; On host: Boyang
> > ; At date: Mon Mar 26 20:15:57 2007
> > ;
> > ; This is your topology file
> > ; Generated by genbox
> > ;
> > ; Include forcefield parameters
> > #include "ffgmx.itp"
> > ; Include water topology
> > #include "spc.itp"
> > #ifdef POSRES_WATER
> > ; Position restraint for each water oxygen
> > [ position_restraints ]
> > ; i funct fcx fcy fcz
> > 1 1 1000 1000 1000
> > #endif
> > ; Include generic topology for ions
> > #include "ions.itp"
> > [ system ]
> > ; Name
> > Generated by genbox
> > [ molecules ]
> > ; Compound #mols
> > SOL 674
> > Everything seems fine here. Then I want to do a MD
> > simulation. I used grompp to get the .tpr. I could
> > also run it. But in the .log file, I found the mass of
> > the system is the mass of H2o ( about 12132) not
> > 13501.164.
> > I got D2O topology from pdb2gmx correctly. But it
> > seems that grompp did not read in this topology.
> > Can anybody kindly tell me where the problem is? What
> > should I do to get D2O topology?
> > Many thanks,
> > Joys Yu
> > ___________________________________________________________________________
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> Dr. Andrés N. McCarthy
> Instituto de Física de Líquidos y Sistemas Biológicos
> Depto. Cs. Biológicas - Fac. de Cs. Exactas - Univ. Nac. de La Plata
> 59-789, CP (1900) La Plata, Argentina
> Tel: +54-221-4254904 / +54-221-4233283
> FAX: +54-221-4257317
> e-mail: amccarthy at iflysib.unlp.edu.ar
> web site: www.iflysib.unlp.edu.ar
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