[gmx-users] Some questions regarding generating topologies

[Manik Mayur]

Hi,

Even though after going through the manual, I still have some basic
confusions regarding generating topologies.

1) I have generated an itp file after adding some Cl- ions using genion. It
goes like this:

[ moleculetype ]
; Name            nrexcl
Cl_ion           0

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1        CL-      1    Cl-     Cl      1         -1     35.453   ; qtot
-1
     2        CL-      2    Cl-     Cl      2         -1     35.453   ; qtot
-2
     3        CL-      3    Cl-     Cl      3         -1     35.453   ; qtot
-3
........
........

To allow nb interactions between all the atoms in the molecule Cl_ion, is
setting nrexcl = 0 okay?

2) In spce.itp provided with GROMACS,

[ moleculetype ]
; molname       nrexcl
SOL             2

while in the manual, on pg. 100 (Chapter-5 Topologies)
[ moleculetype ]
; molname       nrexcl
SOL             1

why is the inconsistency?

3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is recommended).
Since SPC/E is one of the most used model, should I consider using OPLS
rather than GROMOS96, otherwise how significant will be the errors?

4) I am using GROMOS96 43a1, so am I allowed to change combination rule to
'2' ( '1'  is the default). How significantly will it affect the
simulations?

Any relevant idea/suggestion/reference is appreciated.

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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