[gmx-users] Topology file for D2O

Joys Yu joys_yu3 at yahoo.com
Tue Mar 27 08:29:58 CEST 2007

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

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
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
Total mass 13501.164 a.m.u.
Total charge 0.000 e

The total mass for 674 D2O is correct: 674 * 20.03 =

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"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; 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

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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