Dear Rafael, Which version of GROMACS are you using? I cannot guarantee my following comments are valid in 4.6.X, only on 4.0.X and 4.5.X.
What values have you tried from GMX_TPI_DUMP? Basically, the value you set it to will be the energy value that will be compared with the epot of the system with the molecule inserted. Intuitively, I think you're choosing very low values for GMX_TPI_DUMP, as probably the insertion of the water molecule is mostly unfavorable, and the epot is, therefore, hugely large. I'd suggest GMX_TPI_DUMP=1e+20 for a start (be careful, you *will* get a lot of .pdb files: try inserting on a single trajectory frame as a test case and reducing the number of insertions [nsteps]). I don't understand why is your .xvg getting that big, unless you're using a huge trajectory. In tpi(c).xvg, you only have one line per ps, and the GMX_TPI_DUMP doesn't increase the output to the .xvg, IIRC. On another note, I hope you're using the tpic algorithm, with the center of insertion set to the geometric center of your prosthetic group, and not the tpi algorithm. I hope this helps. Best, João On Fri, Aug 30, 2013 at 8:16 PM, Rafael I. Silverman y de la Vega < rsilv...@ucsc.edu> wrote: > Hi all, > I am trying to insert a water into a prosthetic group binding cavity. I > cant seem to get an output .pdb file of the insertions, I set GMX_TPI_DUMP > in my shell with $ export GMX_TPI_DUMP=xxx but no numbers seemed to work. I > cant really get good information out of the .xvg output either, it always > ends up being like 2+ gigs, and is basically unreadable, plus, writing this > file takes a long time, and gums up the processors. > > So 2 questions, can I suppress the writing of the .xvg file, and how do I > get GMX_TPI_DUMP set correctly? > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
