[gmx-users] inclusion of water in gromacs input files

[Chetan Mahajan]

Thanks, Justin. By additional topology details, I meant bond and angle
topology information for each of the water molecules. I have used LAMMPS
before and it is needed there. So  it is not needed here, in Gromacs.

On Wednesday, March 5, 2014, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/5/14, 1:42 AM, Chetan Mahajan wrote:
>
>> Hi,
>>
>> I am new to gromacs and I used acpype (amber2gromacs) tool to generate
>> *.top and *.gro from Amber files *.prmtop and *.inpcrd. For  water, this
>> tool placed following in *.top file:
>>
>>
>> [ moleculetype ]
>> ; molname       nrexcl ; TIP3P model
>>    WAT             2
>>
>> [ atoms ]
>> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>>       1     OW      1     WAT     O      1     -0.834   16.00000
>>       2     HW      1     WAT    H1      1      0.417    1.00800
>>       3     HW      1     WAT    H2      1      0.417    1.00800
>>
>> #ifdef FLEXIBLE
>> [ bonds ]
>> ; i j   funct   length  force.c.
>> 1   2   1   0.09572   462750.4
>> 1   3   1   0.09572   462750.4
>>
>> [ angles ]
>> ; i j   k   funct   angle   force.c.
>> 2   1   3   1   104.520    836.800
>> #else
>> [ settles ]
>> ; i   funct   length-oh length -hh
>> 1   1   0.09572 0.15139
>>
>> [ exclusions ]
>> 1   2   3
>> 2   1   3
>> 3   1   2
>> #endif
>>
>> [ system ]
>>   tio2_wpep
>>
>> [ molecules ]
>> ; Compound        nmols
>>   tio2_wpep        1
>>   NA+                  1
>>   WAT              3656
>>
>>
>>  *My
>> question is it does not include any topology details for 3656 water
>> molecules either in this file or separately. Instead it has topology
>> defined for standard water molecule in atoms section above. However,
>> Gromacs accepted these two files as they are and runs were made. Please
>> comment if I need to include water topology details for all 3656 water
>> molecules. *
>>
>>
> What topology details would you include?  The program simply printed a
> full TIP3P topology, which mimics the effect of #including the tip3p.itp
> file.  It is a complete water topology and needs nothing else.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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