Thanks! I will try these latest suggestions!
On Fri, Aug 30, 2013 at 7:27 PM, Rafael I. Silverman y de la Vega < rsilv...@ucsc.edu> wrote: > 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? 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