indeed it is now working with -center - sorry for not having tried it before ;)
thank you very much Justin, helpful as always!! Nicola On Fri, May 30, 2014 at 2:29 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/30/14, 6:32 AM, Nicola Staffolani wrote: > >> Dear gmx community, >> >> I have a layer of Au atoms to which a molecule is attached. After pdb2gmx, >> when I create the box and put H2O molecules inside using editconf, since >> the planar dimensions of the Au layer are big compared to the >> corresponding >> dimensions of the molecule, I have decided that I want my box to be >> triclinic. >> >> After that I give the box vector lengths a,b and c, I get that along the >> direction perpendicular to the Au layer the box is shifted with respect to >> the system (= Au layer + molecule). In order then to fully enclose the >> system with H2O molecules, what I did is to make the box bigger, but this >> costs time and I would like to understand what is happening and find a >> proper solution. >> >> I have read the gmx online reference about editconf >> <http://manual.gromacs.org/online/editconf.html>: where it is said that >> >> "Both -box and -d will center the system in the box", is the Center of >> Mass >> (CoM) meant?? This would make sense, since my shifted box is shifted >> towards the Au layers, whose Au atoms are much heavier than the atoms of >> the molecule. What I would like to achieve is to geometrically (and not >> gravitationally) center the system inside my box, getting rid in this way >> of the H2O molecules which are under the Au layers. Is there any smarter >> way to use editconf to achieve that without resorting to manually >> eliminating the unwanted H2O molecules? >> >> > You can define whatever position you like with -center based on whatever > box size is appropriate, rather than relying on -box and/or -d, if they are > giving undesirable results. > > -Justin > > > For completeness of information, my executable water.com >> file is: >> >> editconf -f speptide.gro -o -bt triclinic -box 7.2 5.4 6.4 >> genbox -cp out -cs -p speptide -o speptideh >> editconf -f speptideh -o azwater.pdb >> >> Thank you in advance, >> >> Nicola >> >> > -- > ================================================== > > 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. > -- Nicola Staffolani PhD Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics> Università della Tuscia Largo dell'Università s.n.c., I-01100 Viterbo email: n.staffol...@unitus.it tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36 -- 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.
