Hi Pablo, You want to mutually exclusive things. That is by definition impossible.
Sorry, Tsjerk On Mon, Mar 1, 2010 at 11:02 AM, Pablo Englebienne <[email protected]> wrote: > Hi, I made an NpT MD simulation of 10 copies of the same small molecule in > CHCl3 (dodecahedron unit cell) for 20 ns. I want to visualize the evolution > of the system and the distance between the molecules. I tried to visualize > the system, but I can't get a continuous trajectory (i.e., without jumps) > without the solutes diffusing out of the simulation box. The same thing > happens for the inter-molecule distance, it oscillates wildly between a > reasonable value (say, 0.5 nm) and 1/2 the size of the periodic cell. > > When I use trjconv with the "-pbc nojump -ur compact" options, the molecules > diffuse out of the box, in a continuous trajectory, until they are way > further apart than the size of the cell. When visualizing it in VMD, > however, it turns out that not all molecules are isolated, but instead some > are interacting with the periodic image of another molecule. I used "pbc > wrap" from the PBCTools module within VMD and that brings all the molecules > into a single cell, but then the trajectory is not continuous, with > compounds jumping around the edges of the unit cell. It is then not > straightforward to see the interaction among different molecules, as in some > cases they are in opposite edges of the cell. > > If I use the "-pbc mol -ur compact" option, all molecules stay within a > single unit cell, but there are jumps across the border of the unit cell as > in the above case. > > I tried also using the "-center", "-fit rot+trans" and "-fit progressive" > options (with groups containing either all molecules or a single residue) > but this ultimately gave the same results. > > Would there be something else I could try to visualize the simulation so > that the central unit cell would contain all residues in a continuous way? > > Thanks in advance for reading, and more for replying! > > Take care, > Pablo > > -- > Pablo Englebienne, PhD > Institute of Complex Molecular Systems (ICMS) > Eindhoven University of Technology, TU/e > PO Box 513, HG -1.26 > 5600 MB Eindhoven, The Netherlands > Tel +31 40 247 5349 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
