On 10/31/18 11:43 AM, CROUZY Serge 119222 wrote:
Dear gromacs users I've been running gromacs for several years, and enjoyed it.. I've been running PMF calculations for protein DNA interactions without problems until recently: Now I'm puzzled with the X coordinates being written in the pullx files (and thus taken as reaction coordinate values in the PMF). This is my problem I run two simulations 1) protein A moving away from DNA DNA---A-> along x 2) same protein A moving away from DNA in the presence of protein B: B-DNA---A -> along x In 2) A and B interact slightly and I expect to see a slight difference in the profiles for pulling A away In both simulations I'm pulling on center of mass of A away from center of mass of DNA (force along X only) My problem is that the x pulling coordinates in simulation 2) (in the pullx files) are around 9 A larger than in simulation 1). Consequence: the profiles are shifted along x by around 9 A. This is not logical to me since my reaction coordinate is distance between com of A and com of DNA which should be the same !! It's as if the size of the simulation box (around 10 A larger in 2) to accommodate B ) mattered .. ?! (I'm running PME with PBC in water...)
Yes, that makes sense. The first column(s) in pullx.xvg are whatever (x,y,z) components of the group0 COM. If your box is larger, then naturally the position is different. What should not be different is the relative DNA-A distance, which is the actual reaction coordinate. Absolute coordinates of any one species don't really matter.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.