[gmx-users] Some questions regarding generating topologies

[Justin A. Lemkul]

Manik Mayur wrote:
> On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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.
> 
> 
> Thanks for the reply. I will try to follow your suggestion, but just for 
> clarification, setting nrexcl=0 will allow nb interaction between all 
> the atoms in a molecule?

Using nrexcl only applies to intramolecular nonbonded interactions.  There has 
to be some reason with nrexcl = 1 is specified for ions in ions.itp, but that 
may have to do with something in the code.  I suppose, in general, nrexcl = 0 
would include all interactions, but you probably don't want to do that for most 
molecules, since, i.e. neighboring (bonded) atoms interact principally through 
the bonded interaction; nonbonded calculations should not be applied to this 
atom pair.

> 
>         [ 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.
> 
> 
> So the correct version will be nrexcl=2, which means atoms no more than 
> 2 bonds away will be excluded from nb interactions. Is my undestanding 
> correct?
> 

Should be.

-Justin

> 
>         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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================