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

[Justin Lemkul]

On 3/5/14, 2:08 PM, Chetan Mahajan wrote:
> 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.
>

You don't need to define the interactions for every water molecule explicitly, 
no.  That's what Gromacs does for you.  What your WAT [moleculetype] says is, 
"here's everything you need to know about a water molecule."  Then in 
[molecules], grompp maps those interactions to all of the 3656 waters.  The 
software does all the work for you to remove ridiculous levels of redundancy.

-Justin

> 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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-- 
==================================================

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

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