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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