[gmx-users] inclusion of water in gromacs input files
chetanvm10 at gmail.com
Wed Mar 5 20:08:53 CET 2014
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:
>> 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
>> [ settles ]
>> ; i funct length-oh length -hh
>> 1 1 0.09572 0.15139
>> [ exclusions ]
>> 1 2 3
>> 2 1 3
>> 3 1 2
>> [ system ]
>> [ molecules ]
>> ; Compound nmols
>> tio2_wpep 1
>> NA+ 1
>> WAT 3656
>> 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 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
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