[gmx-users] TPIC and GMX_TPI_DUMP

Rafael I. Silverman y de la Vega rsilverm at ucsc.edu
Sat Aug 31 04:27:51 CEST 2013


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 <jmdamas at 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 <jmdamas at 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 <
> > rsilverm at 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 <jmdamas at 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 <
> >> > rsilverm at 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 at gromacs.org
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> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > João M. Damas
> >> > PhD Student
> >> > Protein Modelling Group
> >> > ITQB-UNL, Oeiras, Portugal
> >> > Tel:+351-214469613
> >> > --
> >> > gmx-users mailing list    gmx-users at gromacs.org
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> >> >
> >> --
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> >>
> >
> >
> >
> > --
> > 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 at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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