[gmx-users] Handling of charge and mass fields in topology file produced by x2top

[Steven Kirk]

Hello,

I am using x2top to produce a topology file for a system involving
silica in water, and using the OPLS-AA force field, using the v.3.3-1
CentOS x86_64 RPMS provided on the website (do these contain all the
latest fixes?).

My topology files (suitably edited for brevity, and to insert the atom
type mappings for OPLS-AA), look like this:

;
;       File 'd12bcharged.top' was generated
;       By user: steve (500)
;       On host: onyx
;       At date: Tue Mar 14 18:18:28 2006
;
;       This is your include topology file
;       Generated by x2top
;
; Include forcefield parameters
#include "ffoplsaa.itp"
#define OS opls_179
#define OA opls_154
#define HO opls_155
#define SI SI

[ moleculetype ]
; Name            nrexcl
SNP                 3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
      1         OA      1    SNP      O      0          0         12
  OA          0          0   ; qtot 0
      2         OA      1    SNP      O      1          0         12
  OA          0          0   ; qtot 0

  <and so on until>

    403         SI      1    SNP     SI    402          0      28.08
  SI          0          0   ; qtot 0
    404         SI      1    SNP     SI    403          0      28.08
  SI          0          0   ; qtot 0

  <and later still>

    583         HO      1    SNP   H001    582          0         12
  HO          0          0   ; qtot 0
    584         HO      1    SNP   H011    583          0         12
  HO          0          0   ; qtot 0

What this seems to imply is that x2top seems to recognise a Silicon atom
in the input PDB file and puts the correct mass (28.08) in the topology
file, but seems to be allocating the wrong masses to both the O and H
atoms. I'm now starting to worry that the correct force field parameters
may not have been placed in the topology file either, and hence some
previous simulations runs may be incorrect.

Can anyone suggest a cure ?

In addition, how is the charge field in the [ atoms ] section of the
topology file handled ? If I modify the charge entry for one atom, from,
say, 0 to -1, am I fundamentally breaking the partial charges etc.
specified for that atom by the OPLS-AA force field and hence breaking
the physics ?

Many thanks in advance,

Steve Kirk

-- 
Dr. Steven R. Kirk           <Steven.Kirk at hv.se, S.R.Kirk at physics.org>
Dept. of Technology, Mathematics & Computer Science  (P)+46 520 223215
University West                                      (F)+46 520 223299
P.O. Box 957 Trollhattan 461 29 SWEDEN       http://taconet.webhop.org