Manik Mayur wrote:
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:
This is unnecessary. Just #include "ions.itp" and the parameters for Cl- for
whatever force field you're using are included.
[ 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?
Probably just a typo.
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?
An excellent comparison of different force fields and different water models can
be found in:
Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626.
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?
I would say it invalidates everything. The defaults for combination rules,
bonded parameters, etc. are as much a part of each force field as the atom types
and charges.
-Justin
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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