[gmx-users] Topology file for D2O

[Joys Yu]

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


 


 
____________________________________________________________________________________
Looking for earth-friendly autos? 
Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center.
http://autos.yahoo.com/green_center/