[gmx-users] Topology file for D2O

[Andrés N. McCarthy]

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. 
8064-8067.

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.

Regards

Andrés 


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
(UNLP-CONICET-CIC)
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
----------------------------------------------------------------------