On 4/1/14, 12:56 PM, Kalyanashis wrote:
Thank you Justin for your valuable reply. But you know, my box size is 17.744*17.744*17.744 nm^3. I have used "editconf -bt cubic -f 20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6" to generate the box. And the full description of the box size I have used is "Read 15484 atoms No velocities found system size : 7.604 8.101 13.546 (nm) diameter : 14.544 (nm) center : 2.405 3.212 -2.870 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 6.467 5.661 11.742 (nm) new center : 8.872 8.872 8.872 (nm) new box vectors : 17.744 17.744 17.744 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume :5587.13 (nm^3)" Please suggest me the better option for my system. Should I increase the d value? Actually, the whole system contains approximately 193000 atoms and whenever I am increasing the d value the atoms no. is increasing significantly. Is there any option which can allow me to increase the box size without increasing the number of solvent molecules? And one more more thing, is the cubic option fine?
You're using pressure coupling so the box vectors change over time. The error complains because 8.662854 * 2 = 17.325708, which is totally feasible to expect for normal box vector fluctuations.
A cubic box is usually the most inefficient shape for most systems. Depending on the symmetry of your system, you can probably do a lot better. If you're pulling only along z, then a rectangular box with a suitable z-dimension is probably the next easiest way to go and will save you a ton of unnecessary water molecules.
-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.