[gmx-users] Topology file for D2O
joys_yu3 at yahoo.com
Tue Mar 27 08:29:58 CEST 2007
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
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 water topology
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
; Include generic topology for ions
[ system ]
Generated by genbox
[ molecules ]
; Compound #mols
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?
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