On 3/14/16 6:31 PM, Nash, Anthony wrote:
Hi all, Is there a way of keeping the x, y box dimensions fixed during an NPT simulation, with changes to volume only changing in the Z dimension? Semiisotropic is not quite working out, see below. Context: I want a coiled-coil dimer aligned in the Z direction. Each coiled-coil will see it¹s explicit neighbour, plus all period images. This will give an impression of a collagen fibrillar environment. Each protein should not be be able to tilt off the z-axis, due to the packed nature. Either end of the two coiled coils will be Œbulk¹ water which can expand and contract from changes in volume. If the x or y dimension changes there is a risk to water forming a layer between an explicit coiled-coil and one of its period images, thus losing the fibrillar environment effect.
Set compressibility = 0 for x-y. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
