[gmx-users] Some questions regarding generating topologies

[Justin A. Lemkul]

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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