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

[Justin Lemkul]

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

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