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 <jalem...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.