On 6/1/15 12:07 PM, Victor Ma wrote:
hello Gromacs community, I have a quite embarrassing question to ask. I couldn't find a way to visualize my gromacs trajectory in VMD. There are no tutorial online. By nature, VMD does not recognize Gromacs toplogy file. I see that on Gromacs's website there are two scrippts available: coarse_grain.tcl <http://www.gromacs.org/@api/deki/files/89/=coarse_grain.tcl> and top2psf.pl. For coarse_grain.tcl, I am not sure how to use it. I load it in the TCL console, and nothing happens (no output, no error message). I type in the command ./coarse_grain in both vmd window and tcl console and it just says "invalid command". For the top2psf.pl script, I tried "./top2psf.pl -i topol.top -o topol.psf". It says "Cannot open atoms for reading: No such file or directory". But topol.top is my actual topology file. Please see below: ; Include forcefield parameters #include "charmm36.itp" #include "PROA.itp" #include "POPC.itp" #include "TIP3.itp" #include "SOD.itp" #include "CLA.itp" [ system ] ; Name Title [ molecules ] ; Compound #mols PROA 1 POPC 140 TIP3 8400 SOD 19 CLA 24 So can anyone please do me a huge favor to provide some instruction on how to visualize my gromacs trajectory in VMD or where to find such information.
Load the starting coordinate file, then load the trajectory as data for that molecule. The topology is never involved.
-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.
