I am centering the insertion on the prosthetic group, which I put as 0 0 0. I have a 222 amino acid protein, in maybe .2 M NaCl, I parametrized flavin mononucleotide, which sits inside the protein.
I got the .pdb files written, I was setting the GMX_TPI_DUMP in a different terminal window. Dumb mistake. Here is the first 100 lines from the xvg. The lines go on for a LONG way # This file was created Fri Aug 30 16:54:06 2013 # by the following command: # mdrun -s tpic.tpr -rerun tpic_in.trr -deffnm tpic -nt 1 # # mdrun is part of G R O M A C S: # # GROtesk MACabre and Sinister # @ title "TPI energy distribution" @ xaxis label "\xb\f{}U - log(V/<V>)" @ yaxis label "count" @TYPE xy @ subtitle "number \xb\f{}U > 50: 1.996e+03" @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "direct" @ s1 legend "reweighted" -1445442.50 0 -nan -1445442.40 0 -nan -1445442.30 0 -nan -1445442.20 0 -nan -1445442.10 0 -nan -1445442.00 0 -nan -1445441.90 0 -nan -1445441.80 0 -nan -1445441.70 0 -nan -1445441.60 1 -nan -1445441.50 0 -nan -1445441.40 0 -nan -1445441.30 0 -nan -1445441.20 0 -nan -1445441.10 0 -nan -1445441.00 0 -nan -1445440.90 0 -nan -1445440.80 0 -nan -1445440.70 0 -nan -1445440.60 0 -nan -1445440.50 0 -nan -1445440.40 0 -nan -1445440.30 0 -nan -1445440.20 0 -nan -1445440.10 0 -nan -1445440.00 0 -nan -1445439.90 0 -nan -1445439.80 0 -nan -1445439.70 0 -nan -1445439.60 0 -nan -1445439.50 0 -nan -1445439.40 0 -nan -1445439.30 0 -nan -1445439.20 0 -nan -1445439.10 0 -nan -1445439.00 0 -nan -1445438.90 0 -nan -1445438.80 0 -nan -1445438.70 0 -nan -1445438.60 0 -nan -1445438.50 0 -nan -1445438.40 0 -nan -1445438.30 0 -nan -1445438.20 0 -nan -1445438.10 0 -nan -1445438.00 0 -nan -1445437.90 0 -nan -1445437.80 0 -nan -1445437.70 0 -nan -1445437.60 0 -nan -1445437.50 0 -nan -1445437.40 0 -nan -1445437.30 0 -nan -1445437.20 0 -nan -1445437.10 0 -nan -1445437.00 0 -nan -1445436.90 0 -nan -1445436.80 0 -nan -1445436.70 0 -nan -1445436.60 0 -nan -1445436.50 0 -nan -1445436.40 0 -nan -1445436.30 0 -nan -1445436.20 0 -nan -1445436.10 0 -nan -1445436.00 0 -nan -1445435.90 0 -nan -1445435.80 0 -nan -1445435.70 0 -nan -1445435.60 0 -nan -1445435.50 0 -nan -1445435.40 0 -nan -1445435.30 0 -nan -1445435.20 0 -nan -1445435.10 0 -nan -1445435.00 0 -nan -1445434.90 0 -nan -1445434.80 0 -nan -1445434.70 0 -nan On Fri, Aug 30, 2013 at 5:19 PM, João M. Damas <jmda...@itqb.unl.pt> wrote: > PBC is on works, so the centering is not important. My question had to do > with the center of insertion: random for tpi, specific for tpic. > > That's really my second guess, the infinite energies. The tpi code has a > way to deal with them internally. Run the insertion [mdrun] with "-debug 1" > flag and see how many non-finite energies do you hit. Maybe all (number of > frames times the number of insertions? > > Can you post 100 lines or so of your .xvg file? I'm curious about it. Maybe > 4.6.3 has some new output I'm unaware of. > > Also, can you tell something more about your system? > > Best, > João > > > On Sat, Aug 31, 2013 at 12:55 AM, Rafael I. Silverman y de la Vega < > rsilv...@ucsc.edu> wrote: > > > Thanks for the reply João, > > I am using gromacs 4.6.3, I did centre all 4 frames at the prosthetic > > group. > > I tried GMX_TPI_DUMP = 5.0e+3, 5.0e+20, and even 5.0e-03, still, not a > > single .pdb file written. > > I am doing this on a 4 frame trajectory, consisting of ~7000 atoms per > > frame. I think it may have to do with the frames that have infinite > > chemical potential with the insertion? It doesnt seem to have anything to > > do with TPI_DUMP, when I lower rtpi to 0.05 the .xvg file becomes less > > ridiculously large, only 0.5 gigs... > > I suppose I need to try an older version of gromacs, and see if my setup > > works there > > -- > > 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 > -- 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