Yes, I hand edited the .tpr file to get the thing to work, otherwise I got errors with particle numbers being different.
On Fri, Aug 30, 2013 at 6:54 PM, João M. Damas <jmda...@itqb.unl.pt> wrote: > Sorry, where I said "put it as the last coordinate on the .tpr file you're > building" it should be "put it as the last coordinate of each frame of the > .trr file". You'll need to do some trajectory "hand-editing". > > João > > > On Sat, Aug 31, 2013 at 2:41 AM, João M. Damas <jmda...@itqb.unl.pt> > wrote: > > > Oh, you were talking about the Energy Distribution output (-tpid), sorry. > > So, I haven't used much this output, but from what I see, that energies > > histogram is going indefinitely. It seems like a bug in the calculation > of > > the energy bins, and my intuition is telling me that it has something to > do > > with the volume correction.. Maybe? > > > > My suspicion starts with you saying that you are centering the prosthetic > > group at 0,0,0. That's not the regular procedure for tpi insertions. The > > regular procedure is to center the molecule to insert at 0,0,0. About the > > system, you should calculate the average geometric center of the > prosthetic > > group and use it as the center for insertion! (put it as the last > > coordinate on the .tpr file you're building, see the manual). In short: > be > > careful with your trjconv command and maintain the integrity of the > > trajectory (PBC, wholeness, for example). > > > > Best, > > João > > > > > > On Sat, Aug 31, 2013 at 1:30 AM, Rafael I. Silverman y de la Vega < > > rsilv...@ucsc.edu> wrote: > > > >> 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 > >> > > > > > > > > -- > > João M. Damas > > PhD Student > > Protein Modelling Group > > ITQB-UNL, Oeiras, Portugal > > Tel:+351-214469613 > > > > > > -- > 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