[gmx-users] Some questions regarding generating topologies

[Manik Mayur]

On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul <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?

 [ 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?


>  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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